Hello , I ran a bam file and a sam file through HTSeq for the read counts.
The following the output of the BAM file with no numeric value for the read counts:
And this is the output format from the SAM file:
I am having hard time to interpret these file for the count numbers. The output from the BAM file looks absurd.
The following the output of the BAM file with no numeric value for the read counts:
Code:
krishna@dntdaretouchit:/mnt/e/cannon$ head countread.text XF:Z:__ambiguous[ENSMUSG00000098178.1+ENSMUSG00000106106.2] XF:Z:__ambiguous[ENSMUSG00000098178.1+ENSMUSG00000106106.2] XF:Z:__alignment_not_unique XF:Z:__alignment_not_unique XF:Z:__alignment_not_unique XF:Z:__alignment_not_unique XF:Z:__no_feature XF:Z:__no_feature XF:Z:__alignment_not_unique XF:Z:__alignment_not_unique
Code:
chr1 3206084 255 1S139M = 3206084 -139 NTACAGTTAACCAACTTATACAGTTAACCAACTCCTACACTAGGTTCCTGAGCATTTCCTTAAACTTGCTAGTTCTGGTTTCCTGGCATGTGAGAGTAAGTCACATGGTAGGAGGCTGCCTTTCTATCJJJFJJFJJJAJFJJJFJFFJFJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJA<<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJFFJJJJJFJFJJJJJJJJFJJJJJJJJJJJJJJAFAAA NH:i:1 HI:i:1 AS:i:276 nM:i:0 XF:Z:ENSMUSG00000051951.5 GWNJ-0965:181:GW180227920:7:2124:9881:65265 163 chr1 3206084 255 139M1S = 3206084 139 TACAGTTAACCAACTTATACAGTTAACCAACTCCTACACTAGGTTCCTGAGCATTTCCTTAAACTTGCTAGTTCTGGTTTCCTGGCATGTGAGAGTAAGTCACATGGTAGGAGGCTGCCTTTCTATCATTCAATTTTAGN
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