User: MACRODER

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MACRODER0
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Posts by MACRODER

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Comment: C: How to extract reads/fragments aligned to intergenic regions from bam/sam file?
... Yes, you are right, my input bam was already sorted. I supposed samtools sort was not necessary, but just in case I added it. Green mark checked. Thanks again ...
written 24 days ago by MACRODER0
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Comment: C: How to extract reads/fragments aligned to intergenic regions from bam/sam file?
... Thank you so much. I tried your code with minor modifications and I think it worked perfectly. If anyone ever has the same problem, I used the following: 1-Convert genes.gtf to genes.bed awk -F '\t' '($3=="gene") {printf("%s\t%d\t%s\n",$1,int($4)-1,$5);}' genes.gtf | sort -t $'\t' -k1,1 -k2,2n ...
written 25 days ago by MACRODER0
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How to extract reads/fragments aligned to intergenic regions from bam/sam file?
... Hi. I'm new to RNA-seq data analysis, and I'm trying to extract all reads/fragments aligned in intergenic regions from a sam/bam file. I have a .GTF file with genomic features. I'm working with an organism that does not have introns, so, I would like to use the end position of each gene as a start p ...
sequencing alignment intergenic bam rna-seq written 4 weeks ago by MACRODER0 • updated 4 weeks ago by Pierre Lindenbaum127k

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