HTSeq output file

[kuldeep]

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:

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

And this is the output format from the SAM file:

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

I am having hard time to interpret these file for the count numbers. The output from the BAM file looks absurd.

[luminasapientiae]

I think we need more information.
What is the design of your study? why HTSeq?
I never worked with HTSeq before but i have experience with edgeR, DESeq2 and NOISeq, but i can be more useful if i have more information about your design.

The counts can be extract in R with Rsamtools (look for index function) or in terminal by samtools idsxstats [bam] > [export_to_file]

[GenoMax]

And this is the output format from the SAM file:

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

It looks like you copy/pasted partial lines in this example. Does your example really start with "chr 1". If so you may have a corrupt SAM file.