RSeQC read_distribution zero tag counts for Zebrafish RNASeq data

[Vempalli Fazulur]

Dear RSeQC team,

I aligned Zebrafish data using STAR against GRCz11 genome and tried generating read_distribution summary using bam file.

I downloaded recent release GRCz11 refseq bed file using UCSC Table browser https://genome.ucsc.edu/cgi-bin/hgTables?command=start

And command i used

read_distribution.py -i test.bam -r GRCz11_RefSeq.bed > test.summary.txt

It is assigning 0's to tag counts.

Here is an example summary 

Total Reads                   8773375

Total Tags                    9399504

Total Assigned Tags           0

=====================================================================

Group               Total_bases         Tag_count           Tags/Kb             

CDS_Exons           56165975            0                   0.00              

5'UTR_Exons         11315631            0                   0.00              

3'UTR_Exons         27109869            0                   0.00              

Introns             914381554           0                   0.00              

TSS_up_1kb          30290331            0                   0.00              

TSS_up_5kb          112967730           0                   0.00              

TSS_up_10kb         178598121           0                   0.00              

TES_down_1kb        30395209            0                   0.00              

TES_down_5kb        113703066           0                   0.00              

TES_down_10kb       178459668           0                   0.00              

=====================================================================

Could you please help me to resolve this.

Thanks In Advance

Fazulur Rehaman

[Joshua Wang]

if your BED file is OK, please check if the chromosome IDs are consistent between BED and BAM files. 

Thanks

Liguo 

On Apr 30, 2020, at 5:56 AM, Vempalli Fazulur <vreh...@gmail.com> wrote:



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[Vempalli Fazulur]

Dear Liguo,

Thanks a lot. bed file chromosomes are not consistent with bam. After I remove 'chr' prefix from bed it is working fine.

Thanks & Regards

Fazulur Rehaman

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