Tag: getfasta

Extract fasta sequence from gff3 file

Extract fasta sequence from gff3 file 2 Hi everyone, I have a lot of .gff3 files with the CDS features and below with the fasta sequence. This sequence is separated from the CDS features like this: ##FASTA >NZ_NZ_LR130533.1 I would like to extract all the fasta sequence into new fasta…

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Accepted bedtools 2.31.1+dfsg-2 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 04 Dec 2023 20:13:11 +0100 Source: bedtools Architecture: source Version: 2.31.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1043957 Changes: bedtools (2.31.1+dfsg-2) unstable; urgency=medium . * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957)…

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fasta – Get a certain gene sequence from bam/vcf and reference

I need to get a fasta sequence of a certain gene for a certain worm strain that is different from reference. I have a reference genome, BAM for the strain of interest, and coordinates of the gene. I know that vcftools can convert bam to fasta, but I do not…

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Solved bedtools getfasta -s -fi \$dataCommon/hg38.fa -bed

Transcribed image text: bedtools getfasta -s -fi \$dataCommon/hg38.fa -bed test.bed -fo test.bed.fa bedtools getfasta -fi \$dataCommon/hg38.fa -bed test.bed -fo test.bed.2.fa \# promoter [−5,0] in srand specific manner; ONLY UPSTREAM PROMOTER SELECTION IS POSSIBLE bedtools flank -i test.bed -g \$dataCommon/hg38.chrom.sizes.txt -I 5 -r 0 -s Highlight Both regions having…

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bedtools getfasta chromosome not found

bedtools getfasta chromosome not found 1 I am having the same problem as this post: Trouble with bedtools getfasta When I run the following command, I get this warning for every chromosome and the output fasta is empty: bedtools getfasta -fi GRCm38.p6.genome.fasta -bed e2f5_R1.seacr.peaks.stringent.bed -fo e2f5_R1.seacr.peaks.fasta WARNING. chromosome (1) was…

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Help manually processing strand in paired-end reads when fishing for lariats in bulk RNA-seq

Hi, I’m trying to detect lariat loops in RNA-seq data (circular RNAs produced during splicing). I am following the methods used in Pineda & Bradley 2018 Branchpoint detection algorithm:Our branchpoint detection algorithm was based on the split-read alignment strategy used in Mercer et al. (2015). 1- Prefilter reads:First, filter out…

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ubuntu – ISSUE: malformed BED entry at line 2. Start was greater than end. Exiting. bedtools

I am trying to use bedtools getfasta on a txt file but some of the chromosome coordinates from big to low, how can I fix this so that all chromosome coordinates are from low to big? I am using command line on Ubuntu. I expected the command to run properly…

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Extract CDS reads from a BAM file

Extract CDS reads from a BAM file 1 Hi everyone, I am looking for a way to extract the sequences of the reads that map to the CDS of my reference. I used samtools -b -L CDS.bed BAM.bam > BAM_CDS.bam. That allowed me to get all the reads that overlap…

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Error In Bedtools Getfasta: Chromosome Not Found

I am triing to use BEDtools to get some sequences from genomic coordinates. But I am having an errors saying ” WARNING. chromosome (chr12) was not found in the FASTA file. Skipping.” for each read that I have in my bed file. I gave you some details about what I…

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problem with bedtools getfasta

problem with bedtools getfasta 0 I am trying this code from bedtools getfasta manual: $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ bedtools getfasta -fi test.fa -bed test.bed >chr1:5-10 AAACC # optionally write to an output file $ $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed…

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chromosome identifier not found in FASTA file, prompting ‘skipping’ error, when chr identifier is there

Hi, I have a FASTA file that looks like this: >D00829_0044_ACADL6ANXX_PEdi_Ay_VS_2:6:1214:4434:71826 TGATCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGG >D00829_0044_ACADL6ANXX_PEdi_Ay_VS_2:1:2203:12900:37094 ACTTTGGTCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGG >D00829_0044_ACADL6ANXX_PEdi_Ay_VS_2:1:2213:1470:83635 Which I created through the code below. The .bam file in question is an aDNA file from a Neanderthal (cdna.eva.mpg.de/neandertal/Chagyrskaya/BAM/). samtools bam2fq chr22.rh.bam > chag.22.fq bioawk -c fastx ‘{print “>”$name”\n”$seq}’ chag.22.fq > chag.22.fa I also…

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How to get human cDNA sequences together with UTR regions?

How to get human cDNA sequences together with UTR regions? 2 Dear all, I have downloaded the human genome and gtf files from Gencode. Based on these two files I want to generate a fasta file that has cDNA sequences including 5′ and 3′ UTRs for protein-coding genes only. What…

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[SOLVED] Special .bed to .fa conversion (GenomicCoordinates/DNAsequence) ~ Linux Fixes

My aim is to create a custom protein sequence reference file (protein.fa) from genomic coordinates (origin.bed). (origin.bed; with Chromosome, start, end, TranscriptID, strand, GeneID) chr1 109202569 109202584 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr1 109203584 109203617 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr11 102188276 102188302 ENST00000263464.3_uORF_0 + ENSG00000023445.9 chr11 10830291 10830306 ENST00000530211.1_uORF_1 – ENSG00000110321.11 chr11 10830400…

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bam – Detect mutation context in a read of a sam file

That kind of custom fiddling with reads and variants is very cumbersome, non-standard and also error-prone. Do a standard variant callign pipeline and then filter for the mutations that you want. Then extract the variant position (so the coordinates) and get the variant context from the reference genome. Using individual…

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Trouble with bedtools getfasta

Trouble with bedtools getfasta 0 I am trying to extract sequences from a .fasta file based on a bed file using bedtools getfasta and I am getting the following error. The command run was the following: bedtools getfasta -fi genomic.fasta -bed bedfile.bed -fo output.fasta WARNING. chromosome (chr1) was not found…

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organizing a Bed file for bedtools getfasta

organizing a Bed file for bedtools getfasta 0 I am trying to use bedtools getfasta on some bed files, but the issue is that the peaks bed file columns are mixed up such that the first column with the chromosome names contains the peak location as well for some of…

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bedtools getfasta concatenating sequences

bedtools getfasta concatenating sequences 0 Hi, I have a bed file containing exons of the genes. the name field is specified with name of the gene like (ENSG***). when I run bedtools getfasta I get the sequences of each exon separately. is there a standard way in order to concatenate…

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Exon coordinates and sequence

I did it like that: 1- Download refGene.txt.gz and hg19.fasta from the UCSC goldenpath. ( note: convert hg19.2bit to hg19.fa using twoBitToFa ) 2- Create a bed file with exon coordiniate using my awk script // to_transcript.awk BEGIN { OFS =”t” } { name=$2 name2=$13 sens = $4 ==”+” ?…

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extract entire header from BED file to FASTA

extract entire header from BED file to FASTA 1 Hi, Is there any way one can extract the entire header from a BED file while using bedtools getfasta command and write it in the FASTA output ? Have tried using bedtools getfasta -fi hg19.fa -bed file.bed -fo test.fasta -fullHeader but…

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