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Old 11-27-2017, 10:30 AM   #3
Gazaldeep
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Location: India

Join Date: Nov 2016
Posts: 6
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I used the --very-sensitive option in Bowtie2 while alignment. The use of this option was justified in (https://www.ncbi.nlm.nih.gov/pubmed/27735125 supplementary) to get read counts for homoeologs in wheat. So, this option leads to mapping a read against the best (single) match out of highly identical sequences also..
Is it alright or am I missing something?

Also, generally, when taking transcripts as reference, can't featurecounts be used to get read counts? What other softwares may be used? I'll continue using the in-house perl script for now.
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