How to solve the problem related to unmatched chromosome identifiers?

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3.9 years ago

priya.saxena ▴ 10

While using Featurecounts tool, I am getting zero counts for RNA seq reads, It can be due to unmatched chromosome identifiers in BAM and GTF file. Can someone please help me out in making the identifiers same for both the file?

https://ibb.co/10rT9tL

https://ibb.co/414jkhG

Thank You

RNA-Seq • 851 views

ADD COMMENT • link updated 3.8 years ago by Biostar 20 • written 3.9 years ago by priya.saxena ▴ 10

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How can this be? Usually one uses a reference genome that matches the GTF. What species is this and where are the files from?

ADD REPLY • link 3.9 years ago by ATpoint 85k

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Yes, I used the reference genome and then I did the mapping with Bowtie2 to generate a BAM file. This BAM file and the gtf file from NCBI RefSeq was used as input for Featurecounts. The species used is Desulfovibrio alaskensis G20 from NCBI RefSeq. The FTP link is from where I uploaded GTF and genome sequence to galaxy is the following

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/012/665/GCF_000012665.1_ASM1266v1/

ADD REPLY • link 3.9 years ago by priya.saxena ▴ 10

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Which files did you exactly use?

Try using this for genome: GCF_000012665.1_ASM1266v1_genomic.fna.gz

And this for gtf: GCF_000012665.1_ASM1266v1_genomic.gtf.gz

Both are coming from: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/012/665/GCF_000012665.1_ASM1266v1/