Cannot find a gene in the counts table
I have human rna-seq data and I use the tophat/samtools/htseq pipeline to produce the count table. My problem is that a particular gene, does not appear in the final count table, although it appears on the .gtf file. What could be the reason for that? Shouldn't all genes in the .gtf file appear in the count table?
• 1,031 views
•
link
written
by
felipead66
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Problem to create count file through HTSeq application
written by modarzi
-
RNA-seq: indexing without sorting
written by Rakesh Tiwari •
-
RNA seq library size
written by felipead66
-
How to get gene counts with HTseq
written by Michel Edwar
-
Error on HT-Seq-count while RNA quantification
written by k.kathirvel93
-
Cufflinks gtf file to htseq
written by AP •
-
HTSeq-count wrong reads count
written by ariesliu324 •
-
Is It Possible To Get Features Count Directly From Tophat?
written by samsara
-
Tophat Gene Models Merging
written by Bioinfosm
-
Htseq Count
written by Varun Gupta
Is that only that gene or there are others like that? Did you do any filtering? Does the gene have exons in the GTF? What is the name of that gene? Little more details would be helpful!
Please add code.