Tag: nr

BlastX through Biopython

BlastX through Biopython 0 I have an unknown gene segment in the Human_gene.txt file and I want to run blastx (translated nucleotide) using the blast module of Biopython by making the E-value threshold 0.0001 and displaying the match result of 50 residues of query and subject. I am trying this…

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Split merged Bam file without replacement

Split merged Bam file without replacement 0 Hi guys, I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I’m thinking to merge all…

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Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide | Virology Journal

Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article  Google Scholar  Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…

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biopython – How can i write only a specific elements of the sequences, that i downloaded using Entrez.efetch, to the file( id and sequence itself)

I’m still a begginer at this. I downloaded 20 sequences from NCBI and my task is to allign them with themselves, but I need to separate the data, that I got using Entrez.efetch, so I could use it for allignment and I couldnt write the only specific elements (id and…

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Extensively drug resistant E. coli LZ00114

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

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biopython – How to blastp with fasta file that contains ~50 sequences

I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following: open(“proteins_PROT.fasta”,”r”) from Bio.Blast.Applications import NcbiblastpCommandline cline = NcbiblastpCommandline(query=”proteins_PROT.fasta”, db=”nr”, evalue=0.001, remote=True, ungapped=True) NcbiblastpCommandline(cmd=’blastp’, query=”proteins_PROT.fasta”,…

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peroxisomal multifunctional enzyme type 2-like, maker-scaffold366_size194251-snap-gene-0.19 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Highly Efficient Genome Editing in Plant Protoplasts by Ribonucleoprotein Delivery of CRISPR-Cas12a Nucleases

Review doi: 10.3389/fgeed.2022.780238. eCollection 2022. Affiliations Expand Affiliations 1 Department of Plant Science and Landscape Architecture, University of Maryland, College Park, College Park, MD, United States. 2 College of Agriculture, Nanjing Agricultural University, Nanjing, China. 3 Integrated DNA Technologies, Coralville, IA, United States. 4 U.S. Horticultural Research Laboratory, USDA-Agricultural Research…

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Vertical stratification of the air microbiome in the lower troposphere

Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

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Frontiers | Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study

Introduction Congenital heart disease (CHD) refers to a group of anatomic heart and great vessel malformations that arise during the embryologic development of the fetus. CHD is one of the most prevalent birth defects, affecting around 2.50 out of every 1,000 births in China (1), and it imposes a substantial…

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NCBI looking for testers for a new web-only (for now) clustered `nr` database

News:NCBI looking for testers for a new web-only (for now) clustered `nr` database 0 Find details about how to participate by going to this link. Clustered nr is the standard NCBI nr database clustered with each sequence within 90% identity and 90% length to other members of the cluster. Your…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells

Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM (2014) Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 186:98–109. doi.org/10.1016/j.jbiotec.2014.05.024 CAS  Article  PubMed  Google Scholar  Altamirano C, Illanes A, Casablancas A, Gámez X,…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Error in print &molecular_dipoles under &LOCALIZE in cp2k

May I ask how to print the dipole moment per molecule of the system in cp2k? I tried to do print molecular_dipoles in LOCALIZE:    &LOCALIZE       METHOD CRAZY       USE_HISTORY       &PRINT         &MOLECULAR_DIPOLES           FILENAME…

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speed slow down on running CP2K

Dear All I am newbie in CP2K and trying to run MD simulation on the benzene-water cluster with BLYP functional. I found a strange phenomenon when I check one of the NVE output files with the filename extension of .ener. The CPU time slowed down significantly after step 12283 and…

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ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples | BMC Microbiology

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

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awk command for printing all the repeated matching lines without making them unique

awk command for printing all the repeated matching lines without making them unique 2 I have two files file1 file2 which has taxonomy details . for example file1 : ( it has taxonomy ID – some digit) 9 9 4 4 4 file2 : ( it has other taxonomy details…

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Addition of Ibrutinib to R-Mini-Chop for Newly Diagnosed DLBCL Shows Promise in an Elderly Population

Adding ibrutinib (Imbruvica) to rituximab (Rituxan) plus mini-CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone [R-mini-CHOP]) improved progression-free survival (PFS), quality of life (QOL), and function in elderly patients with diffuse large B-cell lymphoma (DLBCL), according to the primary analysis of the Australasian Leukaemia & Lymphoma Group NHL29 Study presented the 63rd…

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Ibrutinib Plus R-Mini-CHOP Misses OS End Point but Shows Improved PFS in Newly Diagnosed DLBCL

Ibrutinib plus rituximab and mini-CHOP failed to demonstrate a statistically significant improvement in overall survival at 2 years but led to an improvement in progression-free survival, quality of life, and function in elderly patients with diffuse large B-cell lymphoma. Ibrutinib (Imbruvica) plus rituximab (Rituxan) and mini-CHOP (cyclophosphamide, doxorubicin, vincristine, and…

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Tafasitamab and Lenalidomide Combo Yields Higher OS vs Standard Options in Relapsed/Refractory DLBCL

Treatment with tafasitamab (Monjuvi) and lenalidomide (Revlimid) provided an overall survival (OS) benefit vs standard options in a population of patients with autologous stem cell transplant (ASCT)–ineligible relapsed/refractory diffuse large B-cell lymphoma (DLBCL), according to findings from an expanded analysis of RE-MIND2 study (NCT04697160) that was presented at the 2021…

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Bristol Myers Squibb’s Breyanzi (lisocabtagene maraleucel) Significantly Improves Outcomes, Showing Superiority Over 20-Year Standard of Care in Second-Line Relapsed or Refractory Large B-cell Lymphoma Based on TRANSFORM Study Results

PRINCETON, N.J.–(BUSINESS WIRE)–Bristol Myers Squibb (NYSE: BMY) today announced the first disclosure of results from a prespecified interim analysis of the pivotal TRANSFORM study, a global, randomized, multicenter, Phase 3 study evaluating Breyanzi (lisocabtagene maraleucel; liso-cel), a CD19-directed chimeric antigen receptor (CAR) T cell therapy, as a second-line treatment in…

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Liso-Cel Yields EFS Benefit as Second-line Therapy in LBCL

The phase 3 TRANSFORM study (NCT03575351) showed that patients with relapsed or refractory large B-cell lymphoma (LBCL) had a clinically meaningful improvement in event-free survival (EFS) compared with the standard of care (SOC) when treated with liscocabtagene maraleucel (liso-cel), according to prespecified interim results that were presented at the 2021…

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Tafasitamab/Lenalidomide Improves OS Over Other Options in Retrospective Relapsed/Refractory DLBCL

The combination of tafasitamab (Monjuvi) and lenalidomide (Revlimid) prolonged median overall survival (OS) compared with other standard options for autologous stem cell transplant (ASCT)-ineligible patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL), according to a closely matched expanded analysis of the observational, retrospective RE-MIND2 (NCT04697160) study presented at the…

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AYUSH_MALAKAR_HW9.doc – Course IST 687 Assignment HW 9 Name Ayush Malakar Date#library library”kernlab library”ggplot2 library”e1071

############################################### # Course: IST 687 # Assignment: HW 9 # Name: Ayush Malakar # Date: 09/09/2021 # ############################################### #library library(“kernlab”) library(“ggplot2”) library(“e1071”) library(“gridExtra”) #Step 1: Load the data airquality #replacing NA’s with mean values airquality$Ozone[is.na(airquality$Ozone)] <- round(mean(airquality$Ozone, na.rm = TRUE)) airquality$Solar.R[is.na(airquality$Solar.R)] <- round(mean(airquality$Solar.R, na.rm = TRUE)) airquality #Step 2: Create…

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NCBI’s Efetch not working

Any help would be much appreciated. My goal is to run the following for loop to generate a list of sample_id (which is actually isolation site) for a list of SRAs. However I get an error (see below) for each and every SRA. for sra in `awk ‘NR>1{print $1}’ metadata.txt`…

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GitHub – AI-sandbox/gnomix

This repository includes a python implemenation of Gnomix, a fast and accurate local ancestry method. Gnomix can be used in two ways: training a model from scratch using reference training data or loading a pre-trained Gnomix model (see Pre-Trained Models below) In both cases the models are used to infer…

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Mean and SD read length from a range of fastq files

Question: Mean and SD read length from a range of fastq files 2 Hi all, I’m trying to write some code to generate mean read length data from a range of fastq files. awk ‘{if(NR%4==2) print NR”t”$0″t”length($0)}’ HG1.fastq > readLength.txt i’ve got as far as here from looking through other…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?

How can I extract upstream regions in fasta for all blastx hits locally performed on nr database? 0 I have performed blastx on a fasta file. I am trying to extract out the upstream region in fasta for all blastx hits. I will be grateful to you if you can…

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format specifier associated to “description”

BLAST: format specifier associated to “description” 0 I’m using blastx version 2.2.27+ and the subsequent command blastx -db nr -query fasta -outfmt ‘6 qseqid sgi sacc sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle’ -evalue 1e-10 -num_alignments 1 -num_threads 24 -out blast_farm_50_20.txt that give me this…

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ClustalO with multithreading parameter threads appear sleeping

ClustalO with multithreading parameter threads appear sleeping 0 Hello folks, I am running clustalo with threads flag, at the begining clustalo was using the number of threads I specified but when I checked it next day, all of the threads seem sleeping except one. Do you think thats normal, or…

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probable dimethyladenosine transferase-like, maker-scaffold153_size302544-snap-gene-2.18 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of probable dimethyladenosine transferase-like vs. L. salmonis genes Match: EMLSAG00000006273 (supercontig:LSalAtl2s:LSalAtl2s341:673186:674124:1 gene:EMLSAG00000006273 transcript:EMLSAT00000006273 description:”augustus_masked-LSalAtl2s341-processed-gene-6.3″) HSP 1 Score: 484.567 bits (1246), Expect = 2.083e-174Identity = 227/310 (73.23%), Postives = 259/310 (83.55%), Query Frame = 0 Query: 9 KVRKTGSGMSTVEAAGSGGGGQQGMVFNTGLGQHILKNPLVVQSIIDKAALRSTDVVLEIGPGTGNLTVRALEKCKKLIACEVDPRMVAELQKRVQGTHFQSKLQIMVGDVIKTDLPFFDACVANVPYQISSPLVFKLLLHRPFFRCAVLMFQREFAQRLVAKPGDKLYCRLSINTQLLARVDHVMKVGKGNFRPPPKVESSVVRIEPRNPPPPINFKEWDGLTRVAFVRKNKTLGAAFNQTTVLMMLEKNYRVHLSLADEPVPEKIDIKSIIETVLAEIAFKEKRARSMDIDDFMKLLHAFNAKGIHFV 318 KV+ T + GG+QG+VFNT LGQHILKNP VV…

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Gromacs: Class Members – Variables

Gromacs: Class Members – Variables   – n – N : t_UmbrellaWindow , t_bb n : t_coordselection , t_methoddata_kwreal , t_methoddata_permute , t_partition , gmx_fft_fftpack , t_spheresurfacebin , t_methoddata_kwint n_alloc : t_spheresurfacebin n_at_lam : df_history_t n_dev : gmx_gpu_info_t n_dev_compatible : gmx_gpu_info_t nalloc : cu_atomdata , cl_atomdata , gmx_ana_selvalue_t , swap_compartment…

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merge chipseq peaks with bedtools/other tool

# this should do it, concatenate peak locations in all peaks, sort them and merge cat A B C …. | sort -k1,1 -k2,2n | mergeBed -i stdin > locations.bed To know which files the peaks co-ordinates are merged from, you need to have an identifier in each file before…

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SCIRP Open Access

Add your e-mail address to receive free newsletters from SCIRP. Select Journal AA AAD AAR AASoci AAST ABB ABC ABCR ACES ACS ACT AD ADR AE AER AHS AID AiM AIT AJAC AJC AJCC AJCM AJIBM AJMB AJOR AJPS ALAMT ALC ALS AM AMI AMPC ANP APD APE APM ARS ARSci AS ASM BLR CC CE CellBio ChnStd CM CMB CN CRCM CS CSTA CUS CWEEE Detection EMAE ENG EPE ETSN FMAR FNS GEP GIS GM Graphene GSC Health IB ICA IIM IJAA IJAMSC IJCCE IJCM IJCNS IJG IJIDS IJIS IJMNTA IJMPCERO IJNM IJOC IJOHNS InfraMatics JACEN JAMP JASMI JBBS JBCPR JBiSE JBM JBNB JBPC JCC JCDSA JCPT JCT JDAIP JDM JEAS JECTC JEMAA JEP JFCMV JFRM JGIS JHEPGC JHRSS JIBTVA JILSA JIS JMF JMGBND JMMCE JMP JPEE JQIS JSBS JSEA JSEMAT JSIP JSS JSSM JST JTR JTST JTTs JWARP LCE MC ME MI MME MNSMS MPS MR MRC MRI MSA MSCE NJGC NM NR NS OALib OALibJ ODEM OJA OJAB OJAcct OJAnes OJAP OJApo OJAppS OJAPr OJAS OJBD OJBIPHY OJBM OJC OJCB OJCD OJCE OJCM OJD OJDer OJDM OJE OJEE OJEM OJEMD OJEpi OJER OJF OJFD OJG OJGas OJGen OJI OJIC OJIM OJINM OJL OJM OJMC OJMetal OJMH OJMI OJMIP OJML OJMM OJMN OJMP OJMS OJMSi OJN OJNeph OJO OJOG OJOGas OJOp OJOph OJOPM OJOTS OJPathology OJPC OJPChem OJPed OJPM OJPP OJPS OJPsych OJRA OJRad OJRD OJRM OJS OJSS OJSST OJST OJSTA OJTR OJTS OJU OJVM OPJ POS PP PST PSYCH SAR SCD SGRE SM SN SNL Soft SS TEL TI UOAJ VP WET WJA WJCD WJCMP WJCS WJET WJM WJNS WJNSE WJNST WJV WSN YM Read more here: Source link

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Bash operations

Bash operations 3 How to write a bash script that receives ANY integer numbers and print their mean with 2 decimal digit accuracy? Bash • 592 views Here’s one such script: #!/usr/bin/env bash echo ${1} | awk -v RS=” ” ‘{ n++; s+=$0 } END { printf(“%.2fn”, s/n) }’ To…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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NCBI NR protein db nr.gz FASTA inflate error?

NCBI NR protein db nr.gz FASTA inflate error? 0 Hello all, I’m trying to download and makedb for the nr.gz FASTA file from NCBI. I originally used wget ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz to download the nr.gz file. It worked (seemingly). But when I try to run $diamond makedb –in nr.gz -d nr I…

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Remote blast query limit

Remote blast query limit 0 Hello! How many blast queries can be processed by remote blast calls with biopython’s Bio.Blast.NCBIWWW.qblast or BLAST+ with -remote flag? When I go above 1 sequence I get the following message near the top of my XML results file (and no results: internal_error: (Severe Error)…

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Commandline BLAST – errors?

Commandline BLAST – errors? 0 Hi, I’m running command line blastx and blastp against a number of databases. However, running the exact same script on the exact same input files against the exact same databases occasionally seems to output different filesizes. I can only assume that this is because the…

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PROVEAN not working

PROVEAN not working 2 Hello All, I’m having troubles making PROVEAN work. I’m getting this error while trying to run PROVEAN /gpfs01/home/x/NCBI-BLAST/blastdb/ftp.ncbi.nih.gov/blast/db/nr [17:44:08] searching related sequences… [18:45:32] clustering subject sequences… ./provean.sh: line 187: 41879 Segmentation fault $COMMAND Any idea what I’m doing wrong? provean • 652 views • link updated…

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qualimap2 mean mapping quality

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…

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Error in running Demovir

Hi, I am new to bioinformatics and am working on VLP-enriched viral metagenomic datasets and so would like to use Demovir for getting taxonomic annotation on my viral contigs. However, I got an error as follows: Genes predicted, UBLAST complete, sort: No such file or directory, rm: trembl_ublast.viral.txt: No such…

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best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi)

best automated method (unix commandline) to get genome-assembly-accession number for given protein-accession-number (ncbi) 1 What would be the best way (if there is any) to get the accession number of a genome assembly that contains a given protein accession number? E.g. if i just have the results of a blastp…

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Prevalence and Molecular Characteristics Based on Whole Genome Sequenc

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…

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Fastest way to perform BLAST search using a multi-FASTA file against a remote database

Fastest way to perform BLAST search using a multi-FASTA file against a remote database 0 I have a multi-FASTA file having ~125 protein sequences. I need to perform a BLASTP seach against remote nr database. I tried using NcbiblastpCommandline, but the issue is that it only accepts files as input….

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Sequence (annotation) databases in 2021

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…

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Platypus

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…

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Finding 16 mer not present in GRCh38

Thanks for the question – it has kept me busy this Sunday morning / afternoon. As implied by others, this poses a computational challenge but is not insurmountable. For motif searching generally, I usually use AWK. My approach here was to: generate all possible k-mers of the chosen size (run…

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bedGraphToBigWig Tutorial and Report

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations.  1, bedGraph should be without header before sorting awk ‘NR!=1’ input.bedGraph > input.deheader.bedGraph 2, bedGraph should be sorted sort…

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How to visualise a phylogenetic tree with amino acids (double letter repeat) multiple-sequence alignment?

How to visualise a phylogenetic tree with amino acids (double letter repeat) multiple-sequence alignment? 0 I have a fasta file as shown below, rvd.fasta >t1 NI-NG-NR-NN-NG-HD-HD >t_temp5 NG-NG-NI-N*-NR-NI-NN-NG-NG-HD >tal8 NG-NG-NI-N*-ND-NI-NN-NG-NG-H*-NH-NI I have a newick file as follows, tree.newick (tal8:0.49999997,t_temp5:0.47298786,t1:28.37858179); I need to visualise both the tree and rvd.fasta file (multiple-sequence…

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