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Old 11-21-2014, 04:59 AM   #13
Location: Italy

Join Date: Jun 2013
Posts: 13
Default htseq-count: all the counts are 0

Originally Posted by Simon Anders View Post
Are you sure that htseq-count has not given you some error message besides writing an empty file?
Hello Simon

Command used is:
I have passed the sorted bam converted into sam using

samtools sort -n <accepted_hits_chr22.bam> <out_sorted>
samtools view <sorted.bam> <sorted.sam>

Then countng No. of reads per fearture using .gff reference prepared using python script
As the script is not working i.e. giving all counts 0 then I decided to use HTSEQ-count but its also not working:::::::::::

htseq-count -f sam -s no -r name -m union -t exonic_part /home/svashisht/Cariplo_data_analysis_29-05-14/TopHat2_Alignments_CariploData/DNA13058-001-L1/accepted_hits_chr22_sorted.sam /home/svashisht/Cariplo_data_analysis_29-05-14/DEXSeqAnalysis/new.gff >/home/svashisht/Cariplo_data_analysis_29-05-14/DEXSeqAnalysis/DNA13058-008-L1.txt

Warning: 2474344 reads with missing mate encountered.

Results:: pasting head of the results file:

ENSG00000000003 0
ENSG00000000005 0
ENSG00000000419 0
ENSG00000000457 0
ENSG00000000460 0
ENSG00000000938 0
ENSG00000000971 0
ENSG00000001036 0
ENSG00000001084+ENSG00000231683 0
ENSG00000001167 0
ENSG00000001460 0
ENSG00000001461 0
ENSG00000001497 0
ENSG00000001561 0
ENSG00000001617 0
ENSG00000001626 0
ENSG00000001629 0
ENSG00000001630+ENSG00000240720 0
ENSG00000001631+ENSG00000243107 0
ENSG00000002079 0
ENSG00000002330 0
ENSG00000002549 0
ENSG00000002586 0
ENSG00000002587 0
ENSG00000002726 0
ENSG00000002745 0
ENSG00000002746 0
ENSG00000002822 0
ENSG00000002834 0

In the end of the results file

__no_feature 2410288
__ambiguous 23795
__too_low_aQual 0
__not_aligned 0
__alignment_not_unique 2782635

If you have any idea regarding this please help

Thanks in advance


Shikha Vashisht

Last edited by shikha5; 11-21-2014 at 05:03 AM.
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