User: MACRODER

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MACRODER0
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Posts by MACRODER

<prev • 6 results • page 1 of 1 • next >
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stringtie coverage -c parameter?
... I have used stringtie in the novo mode to assemble transcripts from my own RNA-seq data. The code I used was: stringtie input.bam -o transcripts.gtf --rf I visually inspected in IGV the input.bam file, the original annotation file for the genome (from a protozoan poorly annotated) and transcr ...
stringtie coverage transcript assembly written 4 months ago by MACRODER0 • updated 4 months ago by nlehmann100
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Comment: C: Detecting potentially unannotated genes from RNA-seq alignments?
... Thank you, your suggestion was very usefull. I used stringtie and it found many novel transcripts that are not annotated in the refference. I visually inspect in IGV the original bam file and the gtf produced by stringtie, and found that some of the novel transcripts have a really low coverage of RN ...
written 4 months ago by MACRODER0
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Detecting potentially unannotated genes from RNA-seq alignments?
... Hi there. I was hoping someone can help me. I’m new to RNA-seq. I have my own RNA-seq data aligned to the reference genome as a bam file. Since this genome is poorly annotated, I would like to know if there is a way to automatically detect regions that are not present in the gtf annotation file but ...
annotation alignment rna-seq new genes written 4 months ago by MACRODER0
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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 6 months 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 6 months 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 6 months ago by MACRODER0 • updated 6 months ago by Pierre Lindenbaum130k

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