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Old 04-11-2019, 07:18 AM   #1
NDUFB11
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Default Counting and Recount reads with featureCotuns

Hello everyone,

I am using different tools for getting alignments and read count such as,
salmon and STAR.
Both of this tools have reads counted output that I could use directly into DESeq2 for DEG analysis.

My question is, why some pipeline implys the use of featureCouts for counting the reads at the gene level from BAM files if this work have been already done by previous tools used to generate the same BAM?

Maybe I'm missing something ...

Thank you for clarifying
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Old 04-11-2019, 07:23 AM   #2
GenoMax
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Not sure what exactly you are asking. One feeds featureCounts with files that are already aligned. featureCounts only does counting.

Note: featureCounts is part of a larger package called "subread". subread is an aligner that can be used to create BAM files by alignment.
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Old 04-11-2019, 08:03 AM   #3
NDUFB11
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Hi GenoMax,

I performed an alignment with STAR and I have serveal output files.

One output is this:

Sample1ReadsPerGene.out

The counting of the reads is already done by STAR, so why I should use featureCounts to count again the reads using the BAM file from STAR if the counting is already done?

I hope I'm clear

thank you
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Old 04-11-2019, 08:08 AM   #4
NDUFB11
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ok maybe I got it,
if someone wants to choose featureCounts does it otherwise can use the output file.tab of STAR
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