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Forum: Bioinformatics 08-21-2018, 09:34 PM
Replies: 1
Views: 1,901
Posted By garlic
quantifying transcripts in a redundant genome

Hi,

I am trying to quantify the number of reads mapping to genes in a highly redundant bacterial genome (i.e., often several exact gene copies in the genome).

I've mapped reads to genes with...
Forum: Bioinformatics 07-29-2017, 08:21 AM
Replies: 3
Views: 1,882
Posted By garlic
Hi GenoMax. Yes, the chromosome/contig names...

Hi GenoMax.

Yes, the chromosome/contig names are identical between the bam and gtf files. Does featureCounts strictly require another line for each entry that corresponds to a feature, like "exon"?
Forum: Bioinformatics 07-28-2017, 01:33 PM
Replies: 3
Views: 1,882
Posted By garlic
Difficulty using .gtf file in featureCounts read summarization

Hello,

I am doing differential expression analysis on an insect bacterial endosymbiont. I have Illumina HiSeq reads that are paired-end and strand-specific.

I have mapped my reads to a...
Forum: Bioinformatics 02-04-2016, 11:40 AM
Replies: 1
Views: 945
Posted By garlic
Retrieving only Trinity contigs that have mapped reads

Hi,

I am working on the transcriptome of a protist that feeds on another protist (unfortunately, a rather close evolutionary cousin). I have a transcriptome of my target organism mixed with the...
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