Nothing will align with HTSeq?

Question

[Kristin Muench]

Hello,

I'm trying to extract raw count data from a .bam file (output by Tophat2) for use in DESeq2. I'm trying to use HTSeq. Although I can get HTSeq to run, nothing aligns uniquely. The reads themselves are 100 bp long, so I'm surprised that's the case.

I input something like:

htseq-count -f bam -r pos /path/on/cluster/mySampleBam/accepted_hits.bam /path/on/cluster/homoSapGRCh38.gtf

And the output file looks like:

...
ENSG00000282813    0
ENSG00000282814    0
ENSG00000282815    0
ENSG00000282816    0
ENSG00000282817    0
ENSG00000282818    0
ENSG00000282819    0
ENSG00000282820    0
ENSG00000282821    0
ENSG00000282822    0
__no_feature    16996078
__ambiguous    0
__too_low_aQual    0
__not_aligned    0
__alignment_not_unique    2579821

Has anyone had this issue? What might be going on?

I previously sorted the .bam file I'm trying to generate counts for with the command:

samtools sort accepted_hits.bam accepted_hits_sorted

[Devon Ryan]

Just use the -o option and have a look at some of the reads that should be counted. I hope you looked at these in IGV or similar already.

[Kristin Muench]

I haven't - what's IGV? I'm new to this, so any suggestions on how to sanity check as I build my pipeline would be appreciated.

[Devon Ryan]

This is IGV, it's one of a number of viewers for BAM (and other) files. It's always good to have a brief visual look at things when you get weird results. You can then find some reads that should be counted (but obviously aren't), use the -o option and then grep for the read names and see why they weren't counted.

[GouthamAtla]

What's the output of:

samtools view accepted_hits.bam | cut -f5 | uniq -c 

[Kristin Muench]

A very long list of numbers that looks like:

10 0
2 1
1 3
2 0
3 3
1 1
1 3
2 1
1 3
1 0
1 1
1 50
1 1
3 0
1 50
3 3
...

EDIT: It has this many lines: 1566241

[GouthamAtla]

sorry. This command:

samtools view accepted_hits.bam | cut -f5 | sort -n | uniq -c

[Kristin Muench]

Thanks! Output is 4 lines:

1451670 0
1639036 1
2057140 3
33922308 50

[GouthamAtla]

head -5 homoSapGRCh38.gtf
samtools view accepted_hits.bam | head -5

Output?

[Kristin Muench]

For the .gtf file:

#!genome-build GRCh38.p3
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.18
#!genebuild-last-updated 2015-06

For the .bam file:

MG00HS20:702:HYKM2ADXX:1:2209:18725:32851    419    chr1    12042    0    101M    =    12100    159    CAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCA    $$$&(&((*(***+)++*)+))$(%))+)(*)))))))++)))(*++)'*&*%'+++++&))**+"%$%%%%&&&''&''&&'&&&&%%%%&&&&&&&%&#    AS:i:0    XN:i:0    XM:i:0    XO:i:0    XG:i:0    NM:i:0    MD:Z:101    YT:Z:UU    XS:A:+    NH:i:5    CC:Z:chr15    CP:i:102519028    HI:i:0
MG00HS20:702:HYKM2ADXX:2:2108:1447:45504    353    chr1    12058    0    101M    =    12253    296    CACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCAC    &&&(('(&&&(&()+++++++*)++++++)++++++++)*+++&&*+*+++++++++++++++++++*****(((&'''&'&&&&&&&''&&'&&''&&&&    AS:i:0    XN:i:0    XM:i:0    XO:i:0    XG:i:0    NM:i:0    MD:Z:101    YT:Z:UU    XS:A:+    NH:i:5    CC:Z:chr15    CP:i:102519012    HI:i:0
MG00HS20:702:HYKM2ADXX:1:1102:20777:96654    99    chr1    12066    0    101M    =    12100    135    TGGAGTTTCCCTGTGGAGACGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGC    $$$&&%&(***)*))))'+))*()*+)*+++))++&)%'*&*+(&*+++((*)+&)&&)*++++'($%$%%&'&'''&'!#$&$&&&&&&&&&&&%&&&%&    AS:i:-4    XN:i:0    XM:i:2    XO:i:0    XG:i:0    NM:i:2    MD:Z:8T10G81    YT:Z:UU    XS:A:+    NH:i:5    CC:Z:chr15    CP:i:102519004    HI:i:0
MG00HS20:702:HYKM2ADXX:2:1107:5154:17536    355    chr1    12066    0    101M    =    12100    135    TGGAGTTTCCCTGTGGAGACGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGC    $""&&"%&*(****)))*(*+%*)+)+)&(&*')*"%"&&*)'*&&"()+))+***))**+++&***'((('''&'&&'#%&&&'&$&&&&&&%%%$%%%%    AS:i:-4    XN:i:0    XM:i:2    XO:i:0    XG:i:0    NM:i:2    MD:Z:8T10G81    YT:Z:UU    XS:A:+    NH:i:5    CC:Z:chr15    CP:i:102519004    HI:i:0
MG00HS20:702:HYKM2ADXX:1:1102:20777:96654    147    chr1    12100    0    101M    =    12066    -135    GTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAG    $&&&&&&%&$"$$%&&&&&&&'''('&'%)&'+++++++)++++++*(('++*(&*&%*(&)&)*))'+++++++&++*+)++++)*'&*(**&((((&%&    AS:i:0    XN:i:0    XM:i:0    XO:i:0    XG:i:0    NM:i:0    MD:Z:101    YT:Z:UU    XS:A:+    NH:i:5    CC:Z:chr15    CP:i:102518970    HI:i:0

[michael.ante]

I think Goutham Atla wanted to know if the chromosome-naming in your bam file and the GTF are the same: In your sam-file, you have Chromosome One written as chr1. Now you have to look if it's matching with the gtf:

grep chr1 homoSapGRCh38.gtf | head

[h.mon]

and what is the output of:

samtools flagstat accepted_hits_sorted.bam

[Kristin Muench]

39070154 + 0 in total (QC-passed reads + QC-failed reads)
3333382 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
39070154 + 0 mapped (100.00%:-nan%)
35736772 + 0 paired in sequencing
17868386 + 0 read1
17868386 + 0 read2
30998738 + 0 properly paired (86.74%:-nan%)
35736772 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:-nan%)
43100 + 0 with mate mapped to a different chr
19858 + 0 with mate mapped to a different chr (mapQ>=5)