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3.7 years ago
Hi everyone, I am trying to do htseq-count with an in house transcriptome annotation and for some reason is just not working. I get an output with 0 for all the quantifications. Any suggestions? I am running out of ideas.... Thanks !!
samtools view file.bam | head
K00311:84:HYCNTBBXX:1:2227:13971:25034 0 TRINITY_GG_99991_c4_g1_i13.mrna1 144 1 25M * 0 0 CCAGAATTTAGAGCTTTGTCCAGAT AAFFFJJJJJJJJJJJJJJJJJJJJ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:25 YT:Z:UU
K00311:84:HYCNTBBXX:2:1217:21816:46399 0 TRINITY_GG_99991_c4_g1_i13.mrna1 89 1 26M * 0 0 CAGCTCTGACTGTGAGGTGGTGGGCA AAFFFJJJJJJJJJJJJJJJJJJJJJ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YT:Z:UU
K00311:84:HYCNTBBXX:2:2220:23084:27813 0 TRINITY_GG_99991_c4_g1_i13.mrna1 51 1 29M * 0 0 ACTGTCGTACCTCAAGAGCCAAGGTTGGG AAFFFJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:29 YT:Z:UU
head file.gff3
LQNS02276620.1 phaw_gmap_genome CDS 17889810 17889973 98 + 0 ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds1;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 23 186 +
LQNS02276620.1 phaw_gmap_genome CDS 17891693 17891871 99 + 2 ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds2;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 187 365 +
LQNS02276620.1 phaw_gmap_genome CDS 17892279 17892486 100 + 1 ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds3;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 366 573 +
LQNS02276620.1 phaw_gmap_genome CDS 17893338 17893515 98 + 2 ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds4;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 574 751 +
LQNS02276620.1 phaw_gmap_genome CDS 17894428 17894542 100 + 0 ID=TRINITY_GG_99991_c4_g1_i13.mrna1.cds5;Name=TRINITY_GG_99991_c4_g1_i13;Parent=TRINITY_GG_99991_c4_g1_i13.mrna1;Target=TRINITY_GG_99991_c4_g1_i13 752 866 +
htseq-count -t CDS -i Parent -m union -a 0 -f bam file.bam file.gff3 > results_htseq_union_all.txt
Can you show some examples lines where the names match between the two files?
You are right, doing so.