Category: gtf

Technical Support Specialist – BioInformatics – Invitae

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics – Invitae

CrossMap issues changing genome version

CrossMap issues changing genome version 0 I installed CrossMap for conversion of bam, bed, gtf files from one version to another. I use GENCODE so I need to make the files compatible with UCSC browser. I am running into two issues with this tool… If I use following command to…

Continue Reading CrossMap issues changing genome version

Technical Support Specialist – BioInformatics – Invitae (Formerly ArcherDx)

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics – Invitae (Formerly ArcherDx)

GTF upload error UCSC related to stradedness

GTF upload error UCSC related to stradedness 0 Hello, I’m having issues with uploading a .gtf file to the UCSC browser. I am getting the following error: “Error GFF/GTF group STRG.155047.1 on chr12+, this line is on chr12-, all group members must be on same seq and strand” I have…

Continue Reading GTF upload error UCSC related to stradedness

H20 AutoML : kaggle

Search within r/kaggle Read more here: Source link

Continue Reading H20 AutoML : kaggle

Bullsquid game : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Bullsquid game : gmod

Technical Support Specialist – BioInformatics at Invitae

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics at Invitae

What is bigwig file?

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

Continue Reading What is bigwig file?

What files (fasta, GTF) do I need for RNA seq analysis

What files (fasta, GTF) do I need for RNA seq analysis 1 I am very new to programming in general, and I’m trying my best to teach myself R for analyzing RNA-seq data we have. I am using this guide and have gotten to the step where I need to…

Continue Reading What files (fasta, GTF) do I need for RNA seq analysis

replica tool gun : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading replica tool gun : gmod

DEXSeq prepare annotation script throws “object has no attribute ‘next'” for Ensemble GTFs

DEXSeq prepare annotation script throws “object has no attribute ‘next’” for Ensemble GTFs 0 @24764cda Last seen 23 hours ago United States Hi there, I am trying to run the dexseq_prepare_annotation.py script and the code keeps failing after parsing the first line of the gtf. Specifically, the code is failing…

Continue Reading DEXSeq prepare annotation script throws “object has no attribute ‘next'” for Ensemble GTFs

Rsubread FeatureCounts return 0.0% assigned

Using featureCounts in the Rsubread package I am getting 0 annotations. I started from raw sequencing data and the Refseq genome and Refseq Genomic GTF files downloaded from here: www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/ through the download assembly button on the side. I had the top option to RefSeq for both downloads and chose…

Continue Reading Rsubread FeatureCounts return 0.0% assigned

Sexy Gordon Freeman poster. : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Sexy Gordon Freeman poster. : gmod

How can I be sure that raw read counts are well processed from fastq files?

How can I be sure that raw read counts are well processed from fastq files? 0 Hi. I’m new in bioinformatics and try to process fastq files for getting raw read count matrix. I downloaded fastq files from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63452 I used fasterq -dump to download fastq files from SRR Aligned…

Continue Reading How can I be sure that raw read counts are well processed from fastq files?

Sanity check his should never happen

Issues generating the annotated.eff.vcf file : Sanity check his should never happen 0 Hello, I am having a hard time deciphering the error associated with the vcf annotation file. I used the command: java -Xmx8g -jar snpEff.jar Tair10.1 /globalhome/cae453/HPC/sample6.vcf > /globalhome/cae453/HPC/sample6.eff.vcf The output is java.lang.RuntimeException: Sanity check: This should never…

Continue Reading Sanity check his should never happen

Aligning multiple fastq files with genome in one script/one line with STAR

Hi there! This is probably a VERY basic question but I don’t have the best terminal skills so I’m struggling a little. I want to apply what I wrote below for all my fastq scripts without doing a for loop or manually writing the code for each (ideally they all…

Continue Reading Aligning multiple fastq files with genome in one script/one line with STAR

Errors : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Errors : gmod

kallisto genomebam error

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. This is the code that I am using kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o $FOLDER -t 12 –genomebam -g Homo_sapiens.GRCh38.100.gtf.gz -c hg38.chrom.sizes_clean_tab.txt –rf-stranded ${FILES[$i]} ${FILES[$i+1]} My chromosome file looks like that, tabbed and…

Continue Reading kallisto genomebam error

GO BACK TO WORK!! : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading GO BACK TO WORK!! : gmod

Gmod Recon Soldier Art : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Gmod Recon Soldier Art : gmod

cellranger count output does not give all genes.

cellranger count output does not give all genes. 0 Dear all, I have recently started using the cellranger from 10x for scRNA-seq data, after having used my own pipeline (with STAR alignment) for smart-seq2 data, to get the count matrix for then later analyzing with Seurat or Scanpy. I have…

Continue Reading cellranger count output does not give all genes.

kallisto genomebam not showing reads on igv

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. After producing and loading the pseudoalignment bam to the igv, it is empty. This is my initial command: kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o pseudo -t 10 –genomebam -g Homo_sapiens.GRCh38.100.gtf -c hg38.chrom.sizes R1.fastq.gz.trim_1.fq.gz…

Continue Reading kallisto genomebam not showing reads on igv

See how students fused art and science for stunning 2021 PDB Art project

They are the building blocks of life – and their extraordinary structures have inspired these striking artworks from students in Cambridge and beyond. Each year, art students are invited to create pieces based on the Protein Data Bank in Europe (PDBe) – and this year’s work has gone on display…

Continue Reading See how students fused art and science for stunning 2021 PDB Art project

Florida Dark RP Gmod : BrandNewSentence

Search within r/BrandNewSentence r/BrandNewSentence Read more here: Source link

Continue Reading Florida Dark RP Gmod : BrandNewSentence

TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).

TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM). 0 I ran TPMCalculator on my RNA-seq data. This was my first time using this package. It seemed to have done without any problems, but I realized that counts of some genes are zero. I performed DEG analysis…

Continue Reading TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

B.1.620 carries numerous VOC mutations and deletions Lineage B.1.620 attracted our attention due to large numbers of unique mutations in B.1.620 genomes from Lithuania in nextclade analyses (its genomes are 18 mutations away from nearest relatives and 26 from reference strain Wuhan-Hu-1), and those genomes initially being assigned to clade…

Continue Reading Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

dna sequencing – Ficim

Dna Sequencing Fact Sheet National Human Genome Research Institute . Dna Sequencing Wikipedia . Dna Sequencing Video Yourgenome Org . Dna Sequencing Understanding The Genetic Code . Dna Sequencing Genetics Britannica Com . Dna Sequencing Methods Youtube . 2016 News Feature New Study Challenges Gold Standard For Validating . Vollum…

Continue Reading dna sequencing – Ficim

Parsing transcript version in Ensembl mouse annotation

Parsing transcript version in Ensembl mouse annotation 1 Hi all, I aligned some data to a Ensembl transcriptome with novel transcripts. I am trying to lift over the sites from transcriptome to genome, which I have previously done using the R package genomicRanges. The Ensembl FASTA headers look like this…

Continue Reading Parsing transcript version in Ensembl mouse annotation

missing variable in OpenMP clause?

I’m trying to compile the CP2K trunk (revision 12663) with the Intel compiler and OpenMP. I get an error error #6752: Since the OpenMP* DEFAULT(NONE) clause applies, the PRIVATE, SHARED, REDUCTION, FIRSTPRIVATE, or LASTPRIVATE attribute must be explicitly specified for every variable.   [CNT]  in the file pw_methods.F. There are 3 offending…

Continue Reading missing variable in OpenMP clause?

bioinformatics internships for undergraduates

New Bioinformatics Internship jobs added daily. Found inside – Page 396Ann Intern Med. 2002;137:479-486 304. Winters-Hilt, S. Single nucleotide polymorphism and pathogen detection via engineered nanopore modulators. 2011. document.write(‘Report an Issue With This Page‘); Found inside – Page 351Intern. Med. 14, 236–242. 54. Reilly, B. M., and Evans, A. T….

Continue Reading bioinformatics internships for undergraduates

RSEM problem

RSEM problem 0 Good day all! I’m running RSEM as a batch job on a cluster: rsem-prepare-reference –gtf /home/tbeckett/lustre/honours_project/RSEM/ref/Mus_musculus.GRCm39.103.chr.gtf –bowtie2 –bowtie2-path software/bowtie2/2.3.4 /home/tbeckett/lustre/honours_project/RSEM/ref/Mus_musculus.GRCm39.dna.toplevel.fa /home/tbeckett/lustre/honours_project/RSEM/ref/mouse_ref I recieved an error: Transcript ENSMUST00000132294 is out of chromosome 7’s boundary! Any idea what this error might be? Also, the second line when specifying bowtie,…

Continue Reading RSEM problem

Raman spectra with cp2k – details of output files

Hello everyone,  Since I intend to calculate the Raman spectra using AIMD, I followed the tutorial on the cp2k website which uses the .cube files from cp2k and the Travis software for calculating the Raman spectra.  However, after calculating the raman spectra, I get different spectra files:1) spectrum_raman_aniso_ct_ 2) spectrum_raman_depol_ratio_ct_ 3) spectrum_raman_iso_ct_ 4) spectrum_raman_ortho_ct_…

Continue Reading Raman spectra with cp2k – details of output files

Calculating band gap in CP2K

Hi, I am trying to calculate band gap in CP2K for an electrolyte. On the internet, I found two ways to find the band gap. i) Look into one of the .pdos files generated by CP2K and find the energies where the occupation number changes from 2 to 0. Subtract…

Continue Reading Calculating band gap in CP2K

How to filter nanopore transcriptome alignments to trust 3′ ends?

How to filter nanopore transcriptome alignments to trust 3′ ends? 0 I have direct RNA data mapped to the gencode transcriptome with minimap2. Finding the ‘true’ transcript of origin for a read is nontrivial as there are many secondary alignments with very close alignment scores to the primary. After visualising…

Continue Reading How to filter nanopore transcriptome alignments to trust 3′ ends?

How To Convert Bed Format To Gtf?

How To Convert Bed Format To Gtf? 4 Hello, I’ve seen a lot of posts that convert gtf to bed files. However, i have a bed file that I’m trying to convert to gtf. Is there any tool that can convert bed->gtf?? Thanks, convert bed gtf • 19k views •…

Continue Reading How To Convert Bed Format To Gtf?

align_and_estimate_abundance error Trinty

align_and_estimate_abundance error Trinty 0 Hello, I am trying to prepare a reference for alignment and abundance estimation. I have taken the transcriptome fasta file, do I need to use genomic fasta file or gtf file? I don’t understand this point. pl guide me I am using this code perl /cabinfs/opt/applications/trinity/trinityrnaseq-Trinity-v2.5.1/util/align_and_estimate_abundance.pl…

Continue Reading align_and_estimate_abundance error Trinty

SCF calculation can not converge

Dear CP2K community,       I am a new CP2K’s user and recently started to CP2K for calculating a periodic system, like alloy slab. I need to run a geometry optimization, (before this opt step , I had tried use same structure without vacuum ,it can be converged )but…

Continue Reading SCF calculation can not converge

South Africa Job Availability : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading South Africa Job Availability : bioinformatics

Is the Ensembl GRCh38 genome assembly more up to date than the UniProtKB online database?

Dear all, I am working with a list of Ensembl accession codes for a desired group of proteins. I have downloaded the protein annotations related to the genome assembly GRCH38. I fetched the genomic coordinates from UniProtKB API service using the Ensembl accession codes. The service provide a protein annotation…

Continue Reading Is the Ensembl GRCh38 genome assembly more up to date than the UniProtKB online database?

MXene TI2CO2 monolayer GEO_OPT gets stuck

Hello All, I created a Ti2CO2 monolayer (MXene)  that I will attach as an xyz file. I want to run GEO_OPT on this structure with periodic boundary conditions only in the XY directions. In my output RESULTS file  the first SCF converges in 106 steps, but then the file is…

Continue Reading MXene TI2CO2 monolayer GEO_OPT gets stuck

From FASTA to 3D protein? : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading From FASTA to 3D protein? : bioinformatics

How to get the nucleotide sequence through ORF information?

How to get the nucleotide sequence through ORF information? 0 I have a file with ORF information, including the start position and end position on the chromosome. At first I wanted to create a bed file, and then use the getFastaFromBed of bedtools to get the sequence. But I found…

Continue Reading How to get the nucleotide sequence through ORF information?

Answer: Highly mapped to introns

I think your problem is that your bed file doesn’t match the genome/gtf you used. I think it’s too old. My $gtf is the version 104 one like yours. zcat hg19_Ensembl_gene.bed.gz | head chr1 **66999065** 67210057 **ENST00000237247** 0 + 67000041 67208778 0 27 25,123,64,25,84,57,55,176,12,12,25,52,86,93,75,501,81,128,127,60,112,156,133,203,65,165,1302, 0,863,92464,99687,100697,106394,109427,110161,127130,134147,137612,138561,139898,143621,146295,148486,150724,155765,156807,162051,185911,195881,200365,205952,207275,207889,209690, grep ENST00000237247 $gtf 1 havana…

Continue Reading Answer: Highly mapped to introns

Highly mapped to introns

Highly mapped to introns 0 Hi, I am analyzing RNA-seq data from human blood samples. I checked the read distribution using RSeQC read_distribution after mapping by STAR. Usually, I get more than 80% of reads mapped to exons. However, at this time, the result showed only several % were mapped…

Continue Reading Highly mapped to introns

STAR+RSEM pippline without gtf

STAR+RSEM pippline without gtf 0 Dear all, I have question I mapped reads on cds sequence through STAR I don’t have gtf file and want to calculate read count using RSEM but I am stuck by error “RSEM error: RSEM currently does not support gapped alignments” as I don’t have…

Continue Reading STAR+RSEM pippline without gtf

X amino acid in ensembl

X amino acid in ensembl 2 Hello all, I am working on aligning proteins orthologs from different species. I am using the Ensembl API. Strangely, some protein sequences from non-human species have a lot of X. I wonder what does that mean? In theory, if their genome sequence is know,…

Continue Reading X amino acid in ensembl

cp2k9 under cygwin: bomd at graphite: slow?

Good day/good evening everybody: recently I compiled cp2k version 9 under Cygwin,and I am using it with BOMD to try predicting possible favourable orientations of small aromatic molecules next to graphite. I attach here one of trial examples, where a small aromatic moleculeis overwhelmed by the original slightly unfavourable initial…

Continue Reading cp2k9 under cygwin: bomd at graphite: slow?

Extracting exons and transcripts from gff3/gtf

I was just doing something similar about a week ago. You may be able to accomplish this using the GenomicFeatures R package. First load up the following in R: library(GenomicFeatures) library(GenomicRanges) library(rtracklayer) Then you will need to get the chromosome sizes file, which you can generate with directions from this…

Continue Reading Extracting exons and transcripts from gff3/gtf

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

Continue Reading Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Difference between job titles? : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading Difference between job titles? : bioinformatics

Running htseq-count to “grab” long non coding gene_id names

Running htseq-count to “grab” long non coding gene_id names 0 hi all, new to bioinformatics. so bare with me.. I am trying find long non coding RNA from RNA-seq data. As i checked the human gtf file there are 2 different types of long non coding RNA, “lnc_RNA” and “lncRNA”,…

Continue Reading Running htseq-count to “grab” long non coding gene_id names

Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries?

Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries? 0 Hi all, On the GtRNAdb (tRNA-SE analysis) website there is a file containing fasta sequences of different tRNA genes. gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/ I aligned this GtRNAdb database with RNAseq libraries using bowtie2 and got…

Continue Reading Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries?

gffread error

hello I am currently trying to do RNA-seq using public data in brassica juncea. To use htseq-count for making count table, I have to convert gff file which downloaded in brassica database to gtf file. So I used gffread for converting gff file with below command gffread Bju.genome.gff -T -o…

Continue Reading gffread error

wont recognize the gtf or gff3 files (runtime exception)

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

Continue Reading wont recognize the gtf or gff3 files (runtime exception)

Rsubread align maximum nthreads

Hi Experts, I am using Rsubread align using following comand- align (index=”my_index”, readfile1 = “SRR123456_1.fastq” ,readfile2= “SRR123456_2.fastq”, type=”rna”,input_format = “FASTQ”, minFragLength=35,maxFragLength=151,useAnnotation=”TRUE”, nthreads=64, annot.ext = “my_annotation.gtf.gz”, isGTF = “TRUE”, sortReadsByCoordinates = “TRUE”, output_format = “BAM”) here i have asigned 64 threads but in console, i see only 40 threads, I dont…

Continue Reading Rsubread align maximum nthreads

Are there any alternatives to Liftoff

Are there any alternatives to Liftoff – Mapping annotations (GFF/GTF) between assemblies 2 Hi, I am annotating closely related accession (varieties) using reference assembly (please note that I am using only a region, so that is the reason why you don’t see chromosome info). I really liked liftoff (ver 1.6.1:…

Continue Reading Are there any alternatives to Liftoff

convert genomic bigWig file to transcriptome space

convert genomic bigWig file to transcriptome space 0 Hi all, Is anyone aware of a function to convert a bw file mapped to a genome to map to a transcriptome (of said genome), where the input would be the genomic bw file and gff/gtf/bed annotation and output a single ‘transcriptomic’…

Continue Reading convert genomic bigWig file to transcriptome space

STAR align multiple files

STAR align multiple files 1 Hi everybody, I am doing alignment to 36 PE samples using star. to make it little bit easy task I wrote a bash loop to align them all with the same command. here is my loop: for i in $(ls raw_data); do STAR –genomeDir index.150…

Continue Reading STAR align multiple files

List of human protein coding genes with given name (known function?)

List of human protein coding genes with given name (known function?) 2 Hello, To put it simply, I am doing differential expression analysis on human RNA-seq data and I want to focus my analysis of genes that are: 1) Protein coding, so no SNOR or MIR 2) Genes with a…

Continue Reading List of human protein coding genes with given name (known function?)

The bulk modulus of diamond calculated by LAMMPS and CP2K(MM) is very different

Dear All, Firstly, I calculated bulk modulus of diamond by cp2k with QS METHOD, the lattice constant varied from 3.537 to 3.607, then the bulk modulus was calculated to 434.85 GPa by fitting the correlation between volume and energy (Birch–Murnaghan equation of state). And the result matches the real experiment.  Then, I calculated bulk modulus of diamond…

Continue Reading The bulk modulus of diamond calculated by LAMMPS and CP2K(MM) is very different

Blank output When converting GFF3 file to GTF using either gffread or AGAT

Blank output When converting GFF3 file to GTF using either gffread or AGAT 1 Hi, I am trying to convert gff3 file (please see below) to GTF. I used two tools suggested here gffread and agat here. #gff-version 3 Bg_94-1_CX35|chr01_10700000_16500000 Liftoff gene 1 1345 . + . ID=gene_1;Name=Os01g0293800 gene;coverage=0.997;sequence_ID=0.982;extra_copy_number=0;copy_num_ID=gene_1_0 Bg_94-1_CX35|chr01_10700000_16500000…

Continue Reading Blank output When converting GFF3 file to GTF using either gffread or AGAT

tool or database to convert Gene ID to genomic position

tool or database to convert Gene ID to genomic position 1 Hello.I have lots of Pseudogene IDs like LOC100431174 but none of the below methods worked for me to find their genomic position “offline”. I need a table or package to do it offline without querying to a webpage.methods I…

Continue Reading tool or database to convert Gene ID to genomic position

geneiD-genetranscript annotations

Hello, Trying to generate a frame with 2 columns: transcript_id and gene_id, in LINUX (gtf from esembl) grep -P -o ‘ESNCAGd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecag.txt grep -P -o ‘ESNCATd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecat.txt wc -l enseca* # To see if both files have the same length They are not the same length:…

Continue Reading geneiD-genetranscript annotations

How to perform gene annotation in kallisto?

Dear All, I’m Synat, a cancer research student. I’m doing RNAseq experiment looking at differential expression between treatment conditions and looking through pathway analysis too. I’m doing the alignment using kallisto.. I first built index from fasta file and then mapping it to reference gennome using using index and fastq…

Continue Reading How to perform gene annotation in kallisto?

How to get the total genic and intergenic length of a chromosome?

It looks like you have a .gtf file. That means you can extract the exon lines from the .gtf file and count and sum up the exonic intervals. You can generate a sorted .bed file of exon coordinates by: grep -P ‘texont’ your.gtf | cut -f 1,4,5 | sort -k1,1…

Continue Reading How to get the total genic and intergenic length of a chromosome?

cp2k cannot exit from queue when calculates large system being interfaced with ASE

Dear cp2k users and experts, I want to use ASE as a job submission tool on supercomputer and further I plan to use ASE to perform Genetic Algorithm global optimization. However, I find for relatively large system containing more than 200 atoms (generated by GA, so it is always a…

Continue Reading cp2k cannot exit from queue when calculates large system being interfaced with ASE

How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis?

How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis? 0 I am trying to perform STAR alignment and I need the reference files for indexing. I would like to know how to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files so that I can use my following code for indexing…

Continue Reading How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis?

unable to find chromosome in SAM header

featureCounts: unable to find chromosome in SAM header 0 I am using featureCounts to try and create a count table for some RNA-Seq data I collected using an Oxford Nanopore platform. I have .sam files aligned with minimap2, and am running the following command to try to get a count…

Continue Reading unable to find chromosome in SAM header

Your reference doesn’t appear to be indexed. Please run the mkref tool.

cellranger-dna: Your reference doesn’t appear to be indexed. Please run the mkref tool. 1 I received the following error when running cellranger-dna: “Your reference doesn’t appear to be indexed. Please run the mkref tool”. The reference that I used was downloaded from 10X database. I thought the reference was already…

Continue Reading Your reference doesn’t appear to be indexed. Please run the mkref tool.

Transcriptional noise detection and Salmon TPMs

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

Continue Reading Transcriptional noise detection and Salmon TPMs

More than one archive specified. Try –help.

Package: routine-update Version: 0.0.6 Severity: important Hi Andreas, when working on making sure the python-biopython watch file was appropriately fixed, I saw routine-update choke with the following error: $ routine-update gbp:info: Fetching from default remote for each branch gbp:info: Branch ‘master’ is already up to date. gbp:info: Branch ‘pristine-tar’ is already up to date. gbp:info: Branch…

Continue Reading More than one archive specified. Try –help.

Cousin Match through GEDMatch – Fred Krause

Fred is the closest match to my family through 23andme. I thought he was decended from Ebenezor who would be my great grandfather Ishmaels brother. A Jane Devota from New Lothrup Michigan only a few miles from my home town Chesaning is decended from Ebenezor also. Her mother was a…

Continue Reading Cousin Match through GEDMatch – Fred Krause

Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

Continue Reading Bioconductor Forum

When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

Continue Reading When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Mapping reads and quantifying genes

Mapping reads and quantifying genes – Metagenomic workshop 0 Hello, I am using the following metagenomic workshop tutorial to analyse my own metagenomic data. metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html I performed the following steps: mapped reads with bowtie2 and generated .bam file with samtools sort. Removed duplicates with picard Extracted gene information from prokka…

Continue Reading Mapping reads and quantifying genes

local variable ‘feature_db’ referenced before assignment

Hi, I want to map annotations from rich gencode human gtf or gff3 to great apes’ genome. I tried to run liftoff (github.com/agshumate/Liftoff) but it returns error the below. Following the github issue’s post, I confirmed there’s no _db file before running, the annotation file is .gff3, the permission of…

Continue Reading local variable ‘feature_db’ referenced before assignment