htseq-count returns 0 count for all
1
0
Entering edit mode
16 months ago
ziziqolo ▴ 10

HI biostars

I'm struggling a problem. I want to make count with htseq-count,

10 bam files, aligned with hisat2 (alignment rate 60% - 80%),

sorted by samtools,

both fna file and gff downloaded from ncbi (one species),

head of bam file:

@HD     VN:1.0  SO:coordinate
@SQ     SN:chrNC_037328.1       LN:158534110
@SQ     SN:chrNC_037329.1       LN:136231102
@SQ     SN:chrNC_037330.1       LN:121005158
@SQ     SN:chrNC_037331.1       LN:120000601
@SQ     SN:chrNC_037332.1       LN:120089316
@SQ     SN:chrNC_037333.1       LN:117806340
@SQ     SN:chrNC_037334.1       LN:110682743
@SQ     SN:chrNC_037335.1       LN:113319770
@SQ     SN:chrNC_037336.1       LN:105454467

the first row of gff file is:

NC_037328.1 RefSeq  region  1   158534110   .   +   .   ID=NC_037328.1:1..158534110;Dbxref=taxon:9913;Name=1;breed=Hereford;chromosome=1;gbkey=Src;genome=chromosome;isolate=L1 Dominette 01449 registration number 42190680;mol_type=genomic DNA;sex=female;tissue-type=left lung

code I used for htseq:

htseq-count -t gene -i gene file.sorted.sam annotation.gff > file.txt

htseq-count -s yes -t gene -i ID file.sorted.sam annotation.gff > file.txt

even --idattr=gene and --idattr=exon and -i Parent -i transcript_id but all of these just return 0 count or error.

would you please help me?

any answer is appreciated.

many thanks

RNA-Seq htseq-count • 403 views
ADD COMMENT
3
Entering edit mode
16 months ago

You have to make sure the sequence naming is exactly the same in your GFF as in you fasta file you use to align it to.

In you specific case : NC_037328.1 != chrNC_037328.1

ADD COMMENT
0
Entering edit mode

Thank you Dear lieven.sterck. you solved my problem.

ADD REPLY

Login before adding your answer.

Traffic: 1879 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6