featureCounts: 0% successfully assigned fragments
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KMS • 0
@de2afa3c
Last seen 2 days ago
Croatia

featureCounts: 0% successfully assigned fragments on PE .BAM files

I am facing same problem, performed every suggestion but unable to get map reads I am working on microbial RNA seq data if changing name of headers is solution please suggest how to that. and why Meta-features : 87

featureCounts Returns 0.0% successfully assigned fragments

featureCounts • 212 views
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Lack of any details, not appreciated. Anyway, are chromosome identifiers the same between BAM and GTF?

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Sorry for the incomplete information. I have bacterial RNASeq pair end data and using subread/Rsubread on Rstudio and ubuntu, after few seconds it show results as "featureCounts: 0% successfully assigned fragments". I have checked BAM file in linux it seems ok, I have no idea whats happening.

Yes as per your comment I think chromosome identifiers are same. The headers of sorted BAM file and GTF are same. Although in gtf below the header following information is available. gtf-version 2.2

!genome-build ASM….

!genome-build-accession NCBI_Assembly

!annotation-date 02/12/2022 06:46:27

!annotation-source NCBI RefSeq

Is "!" before genome/annotation problematic ?

in gtf seq starts from NZ_CP042... while in BAM from NS50068

I also tried htseq and getting following results 6382325 alignment record pairs processed. no_feature 2436902 __ ambiguous 0 __ too_low_aQual 50447 __ not_aligned 3894976 __ alignment_not_unique 0

Kindly suggest

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What you have to do is to check whether the chromosome names in the BAM file are part of the GTF. Do it programatically, not by eye. Extract them from the BAM, and from GTF, and then compare and make sure all of the BAM chromosomes can be found in the GTF.

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Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% successfully assigned fragments, and ht-seq giving me output file but similar file so I cant use it in the downstream deseq2 analysis Kindly suggest Thanks

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