Dear All,
I encountered a problem in htseq-count when running
with the command:
got the warning messages for every read.
Here are some information for my sam and gtf file.
And finally, getting all of zero counts for every gene like below:
Anyone who encountered this problem before or who can advise me in details to address this?
It would be very appreciated for feedback from you guys!!!
I encountered a problem in htseq-count when running
with the command:
Code:
python -m HTSeq.scripts.count /home/accepted_hits.sam /home/ref_annotation.gtf --stranded=no > /home/readcount.txt
Code:
: : : Warning: Skipping read 'SRR064199:1:120:5973:2700#', because chromosome 'ZZEF1', to which it has been aligned, did not appear in the GFF file. Warning: Skipping read 'SRR064199:1:100:15531:20305#', because chromosome 'ZZEF1', to which it has been aligned, did not appear in the GFF file. Warning: Skipping read 'SRR064199:1:81:15517:14126#', because chromosome 'ZZEF1', to which it has been aligned, did not appear in the GFF file. Warning: Skipping read 'SRR064199:1:84:2264:2294#', because chromosome 'ZZEF1', to which it has been aligned, did not appear in the GFF file. Warning: Skipping read 'SRR064199:1:16:2321:19643#', because chromosome 'ZZEF1', to which it has been aligned, did not appear in the GFF file. 8987862 sam lines processed. : : : while it is running, such warnings are coming out on and on.
Code:
dhcp128036164097:~ $ head -10 accepted_hits.sam @HD VN:1.0 SO:coordinate @SQ SN:1433E LN:1456 @SQ SN:1433F LN:1767 @SQ SN:1433G LN:2842 @SQ SN:1433S LN:1340 @SQ SN:1433T LN:1803 @SQ SN:1433Z LN:3600 @SQ SN:2ABB LN:1631 @SQ SN:3BHS LN:1521 @SQ SN:3BP5L LN:3264
Code:
hcp128036164097:~ $ head -10 ref_annotation.gtf chr1 oviAri1_refFlat stop_codon 2625590 2625592 0.000000 - . gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat CDS 2625593 2625786 0.000000 - 2 gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat exon 2625494 2625786 0.000000 - . gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat CDS 2626259 2626358 0.000000 - 0 gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat start_codon 2626356 2626358 0.000000 - . gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat exon 2626259 2626400 0.000000 - . gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat exon 2628330 2628369 0.000000 - . gene_id "PRLH"; transcript_id "PRLH"; chr1 oviAri1_refFlat stop_codon 2635951 2635953 0.000000 - . gene_id "MLPH"; transcript_id "MLPH"; chr1 oviAri1_refFlat CDS 2635954 2635977 0.000000 - 2 gene_id "MLPH"; transcript_id "MLPH"; chr1 oviAri1_refFlat exon 2635892 2635977 0.000000 - . gene_id "MLPH"; transcript_id "MLPH";
And finally, getting all of zero counts for every gene like below:
Code:
ABCG2 0 ABHD5 0 ACACA 0 ACLY 0 ACTB 0 ACVR2A 0 ADCYAP1 0 ADIG 0 ADORA3 0 ADRB2 0 ADRB3 0 AGPAT1 0 AGTR1 0 AHSG 0 AIMP2 0 AK1 0 AKT1 0 ALB 0 ALDH1A1 0 ALDOB 0 AMP18 0 ANXA2 0 APOBEC3F 0 APOBEC3Z1 0 APOBEC3Z2 0 APOBEC3Z3 0 AQP1 0 AQP4 0 AQP5 0 ARAF 0 ARF1 0 ARF3 0 ARF4 0 ARF5 0 ARF6 0 ARFIP2 0 ARFRP1 0 ARL1 0 ARL2 0 ARL2BP 0 ARL3 0 ARL4A 0 ARL4C 0 ARL5A 0 ARL5C 0 ARL6IP1 0 ARL8A 0 ARL8B 0 ARNTL 0 ASF1A 0 ASIP 0 ASZ1 0 ATF4 0 ATOX1 0 : : :
Anyone who encountered this problem before or who can advise me in details to address this?
It would be very appreciated for feedback from you guys!!!
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