User: Javad

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Javad60
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Posts by Javad

<prev • 49 results • page 2 of 5 • next >
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problem in running cutadapt on multiple cores
... Dear all, I am trying to use cutadadpt for trimming adapters. It works perfectly when I run it on single core but when I try to use it on multiple cores I get the following error. ERROR: Traceback (most recent call last): File "/home/user/.local/lib/python3.6/site-packages/cutadapt/pipel ...
rna-seq written 11 months ago by Javad60
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How to remove primers from a sequencing run with cutadapt
... Dear all, I would like to use cutadapt to trim the primers from my sequencing run. I was just wondering when I give the sequence of my primer to cutadapt, do I also have to give the complementary sequence as well? for example let's say my primer is: AATC Then is this command "`cutadapt -g AATC in ...
rna-seq written 11 months ago by Javad60
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SNPs identification in Human
... Dear all, I would like to ask you a question regarding identification of SNPs in individuals. I have the exome sequence of around 20 individuals (Human) and I would like to identify the SNPs in the exome of theses persons. I have never worked with SNPs before so I would be grateful if somebody c ...
rna-seq written 12 months ago by Javad60 • updated 12 months ago by genomax67k
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differences in different versions of genomic assemblies
... Hello everybody, Could you please explain what is the difference between different versions of genomics assemblies. I am particularly interested to know when a new version of genomic assemblies is published (for example GRCh37 vs GRCh38), does the coordinates of different genomic features change or ...
rna-seq written 13 months ago by Javad60 • updated 13 months ago by genomax67k
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Comment: C: SNPs in 1000 genome project
... I don't think it would be just a single command. because the coordinates of exons are not included in the vcf file. Am I missing some thing? Could you please give me some hints to go through it? Thanks ...
written 13 months ago by Javad60
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Comment: A: SNPs in 1000 genome project
... Yeah, But I didn't want to write scripts. I thought maybe this data is already stored somewhere. Thank you anyway. ...
written 13 months ago by Javad60
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SNPs in 1000 genome project
... Hello every body, I want to have SNPs of 1000 genome project only for exons. The database of 1000 genome project includes SNPs for the whole genome. Is there an easy way to filter and download data only for exons. I don't want to spend time on writing scripts to filter data. I would be grateful if ...
snp written 13 months ago by Javad60 • updated 13 months ago by Alex Reynolds28k
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Comment: C: How to run cutadapt in parallel
... I ran this one for example: > parallel -k -j 24 cutadapt -u 15 -o output.fastq input.fastq What can I change to make it right? Thanks a lot... ...
written 15 months ago by Javad60
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How to run cutadapt in parallel
... Hi everybody, I am using cutadapt to trim and QC of my NGS data but it is damn slow. I have also installed GNU Parallel to run it in parallel but I couldn't. To be honest, the tutorial of GNU Parallel is so complicated and I couldn't figure out how to run cutadapt in parallel with it. let's assume ...
rna-seq written 15 months ago by Javad60 • updated 14 months ago by Biostar ♦♦ 20
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Genome annotation of mouse that only includes long non coding RNa
... Hello every body, I am working with RNA seq data that is coming from mouse. I am interested only in long non-coding RNA genes in mouse but I can not find an annotation file that only includes long non coding RNAs. Can anybody sugges a link or address that I can use to find this type of annotation f ...
rna-seq written 17 months ago by Javad60 • updated 17 months ago by genomax67k

Latest awards to Javad

Popular Question 18 days ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to manipulate a gff or gtf file manually?
Popular Question 3 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 3 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Great Question 6 months ago, created a question with more than 5,000 views. For looking for an R package for GO term analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For Converting GTF file to UCSC-styled bed file
Popular Question 6 months ago, created a question with more than 1,000 views. For looking for an R package for GO term analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA spike-ins: Their applications and bioinformatics methods for the analysis
Popular Question 9 months ago, created a question with more than 1,000 views. For htseq-count output file
Popular Question 9 months ago, created a question with more than 1,000 views. For htseq-count output file
Popular Question 11 months ago, created a question with more than 1,000 views. For looking for an R package for GO term analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For looking for an R package for GO term analysis
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