getting dexseq_count.py to work

[alpesh]

Hi,

Can you help me in this? I have paired end reads in sam format, and I have followed all steps to create the sorted sam file according to the passilla tutorial. I have successfully created the maize gtf file using the first python script. This is how my sam file looks like,

GALZUI2_0001:8:100:0:142#0/1	4	*	0	0	*	*	0	0	NCCTGGTGGAGACCGGAGGAGCCTCGGCAGAGATCG	#0--011+++858::7=386>?;=:9?9==8??###	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:0:1654#0/1	16	chr1	128019411	0	35M1S	*	0	0	TTTTCTCTGTTGATATTTCAATCTTCTTCCTCAGAN	FFFFFFFFFFFFFF=FFFFFF??===44574,,00#	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:0:1914#0/1	0	chr5	84824688	0	1S24M240N11M	*	0	0	NTTTGCAGCTGATGCTGAGAGCAAGATTGTCCCTGC	####################################	MD:Z:8X26	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1	YS:A:+
GALZUI2_0001:8:100:0:1953#0/1	4	*	0	0	*	*	0	0	NCATAAACGATGCCGACCAGGGATCAGCGAGATCGG	####################################	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:0:1957#0/1	0	chr8	166503511	0	1S35M	*	0	0	NACAAGGTAGGCCTCAGCCGCCTCCTGCAGCGCGGA	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:0:2018#0/1	0	chr8	48995004	0	1S35M	*	0	0	NAAGGGTATAACATCTCTGATGTTCTCCATTCCGGT	#/-,+//.,,9:???==<<=FFF<<=:=?=881:8=	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:2	NH:i:2	YR:i:1
GALZUI2_0001:8:100:0:2018#0/1	0	chr8	49024165	0	1S35M	*	0	0	NAAGGGTATAACATCTCTGATGTTCTCCATTCCGGT	#/-,+//.,,9:???==<<=FFF<<=:=?=881:8=	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:2	NH:i:2	YR:i:1
GALZUI2_0001:8:100:0:287#0/1	4	*	0	0	*	*	0	0	NCGGGGTTTCTTATGCGTGGATCCGGGAGATCGGAA	####################################	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:0:356#0/1	0	chr8	175216115	0	1S35M	*	0	0	NTCGAATACATGTCCTCTCTTCTGGTTCAGAACACC	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:0:362#0/1	4	*	0	0	*	*	0	0	NAACAGCATGGATCCACCTTTTTCCCAACCTTTGAG	#*+('(++)+8::::1:60:==:<;=====FFF;FF	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:0:434#0/1	16	chr1	300430123	0	35M1S	*	0	0	ACCTTACTCTATGCAAGGCATGCCTTACTATCCTGN	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:0:596#0/1	0	chr2	104752145	0	1S35M	*	0	0	NGATGTGGTTGCGAAGAATGGCATGACGATGGTTGA	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:4	NH:i:4	YR:i:1
GALZUI2_0001:8:100:0:596#0/1	0	chr4	68856217	0	1S35M	*	0	0	NGATGTGGTTGCGAAGAATGGCATGACGATGGTTGA	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:4	NH:i:4	YR:i:1
GALZUI2_0001:8:100:0:596#0/1	0	chr5	193863017	0	1S35M	*	0	0	NGATGTGGTTGCGAAGAATGGCATGACGATGGTTGA	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:4	NH:i:4	YR:i:1
GALZUI2_0001:8:100:0:596#0/1	0	chr9	90763379	0	1S35M	*	0	0	NGATGTGGTTGCGAAGAATGGCATGACGATGGTTGA	####################################	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:4	NH:i:4	YR:i:1
GALZUI2_0001:8:100:1000:1005#0/1	16	chr1	31201451	0	36M	*	0	0	AAATATGGCACATATCAGGTGAACAGTGACCAAAAC	=886A<A?8)CEB=.CFEF88>CEHHDHBHEEEGEG	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1011#0/1	4	*	0	0	*	*	0	0	GCTACATCGACCTTTCGAAGCGTCGCGAGATCGGAA	AGEFBAEGGGECFHHHGCHDHHHFFHDHFHHH?HBC	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1039#0/1	4	*	0	0	*	*	0	0	TCTCATGTGATGAGAAGTAGAACTAGTGGAGAGATC	FFFFF:FFEF4EBFGFE>FFEFFFFFFFFFFFFFFF	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1073#0/1	4	*	0	0	*	*	0	0	ACCAGAGCCTGTCCGTGGATGGGACCGGAGATCGGA	HHEEHCHEHEGFHHEE=H/HEH9DHFEEF?=@GA##	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1076#0/1	4	*	0	0	*	*	0	0	GACAAGTTGGCCCACCAGAATATGAGCCTACAGGAA	GH1HHHEHHHHHHHFFFF6FFFFFFFF?FFF-FEF<	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1089#0/1	4	*	0	0	*	*	0	0	GCTCGATGGCGGATGAAAATCAGGCAGATCGGAAGA	HHCHHEHDHHF@EFF6=C;AE?BFFEE?EFBDA?FF	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1099#0/1	16	chr9	15614973	0	2S34M	*	0	0	TCTCAACGTTTGAAGAAAAACCGTGAGATATACCGG	8HHHGHGE=BCHHHHFGDB6EHFGEHHBDHD?GFFG	MD:Z:34	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:11#0/1	4	*	0	0	*	*	0	0	GTGGAGACGCAGGCGTGGAAGAGATCGGAAGAGCGG	AAA@>6>@/<DG;C?GGGDGGCGGCEEGEGGGGAGG	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1145#0/1	0	chr6	147883848	0	32M4S	*	0	0	ATTGTCGGCAACGGCGGGAAGCACCGCTGCCCCGCC	FGFG>DDHDHGEFADA####################	MD:Z:32	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1173#0/1	16	chr1	269036723	0	36M	*	0	0	TGTCAGGGACATGAAGGAGAAGCTCGCCTACATTGC	FD?BDFCC?6<<CC@>C6:1AGGEAG???7@AAC@=	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1195#0/1	16	chr3	135445725	0	36M	*	0	0	ACGGCGCCTGCCGCAAAGATCATAGATACAGTTGGA	###@?=6.GGCCGGGFG6GDGGGGGCGGCGGGGGGG	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:121#0/1	0	chr3	3313715	0	34M2S	*	0	0	GCCTCACTGAATATTCCAGCAGCTGTTGGCTGGGAG	HHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHFGH	MD:Z:34	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:121#0/1	0	chr8	25015676	0	34M2S	*	0	0	GCCTCACTGAATATTCCAGCAGCTGTTGGCTGGGAG	HHHHHHHHHHIHHHHHHHHHHHHHHHHHHHHHHFGH	MD:Z:34	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:121#0/1	16	chr4	63782093	0	2S34M	*	0	0	CTCCCAGCCAACAGCTGCTGGAATATTCAGTGAGGC	HGFHHHHHHHHHHHHHHHHHHHHHHIHHHHHHHHHH	MD:Z:34	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:1217#0/1	16	chr10	68420921	0	36M	*	0	0	ACCTGAAGAGTGTTAGGGAATTGATCTACAAAAGAG	50?EEEGEGEGEEBGED??@;CDGGDC?CCBBD=DD	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1249#0/1	0	chr1	222562953	0	36M	*	0	0	AAAGGATGAGACCAGAGAATCATAGCAATCAGCTCA	HHGCHH@HHGDHHEHAGE5GHHHHHHF7HHHHEHHE	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:1249#0/1	16	chr2	41634471	0	36M	*	0	0	TGAGCTGATTGCTATGATTCTCTGGTCTCATCCTTT	EHHEHHHH7FHHHHHHG5EGAHEHHDGHH@HHCGHH	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:1249#0/1	16	chr5	161906550	0	36M	*	0	0	TGAGCTGATTGCTATGATTCTCTGGTCTCATCCTTT	EHHEHHHH7FHHHHHHG5EGAHEHHDGHH@HHCGHH	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:3	NH:i:3	YR:i:1
GALZUI2_0001:8:100:1000:1371#0/1	0	chr10	89544264	0	35M1S	*	0	0	CTTATGCTTCACTTTTACTATAGGCTCAGAACTTTT	GGGFAHHHHHHHHHHHHGGHHHHGHHHGHHHHHHHE	MD:Z:35	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1465#0/1	4	*	0	0	*	*	0	0	CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTT	>BBEEBEEEF3FCC@FFFEFFFFFBFEFFF=FBFFE	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1489#0/1	16	chr2	176558351	0	36M	*	0	0	CGTGACAAGTGCAGGAAACAAACCACTGAAAAGAAT	@=DA@6F<<@>F?DDG>7C=?6==4;A@6ADEBEBE	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1496#0/1	4	*	0	0	*	*	0	0	CCAGATCAGCGTCGACTCATTTCGGGAGATCGGAAG	GHEHHHHHFHGGGG??AG=GEGGGGGGGDGBGEGGE	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1536#0/1	16	chr9	94009423	0	36M	*	0	0	AGTCAAATGTAACAACTGGTTTTAGCTTGATCTCTT	FHHHHHHGHHHEHHHHFHHHHHHHGHHHHHHHHHHH	MD:Z:36	RG:Z:s_8_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:8:100:1000:1555#0/1	4	*	0	0	*	*	0	0	CGTCGTTGGGGTAGTAGACGGCAGATCGGAAGAGCG	FFBBFFHHHFHHHFEHHHHAHHHHHFDHHHFHHGHH	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped
GALZUI2_0001:8:100:1000:1559#0/1	4	*	0	0	*	*	0	0	GCAGATTTCACCAAGTGTTGGATTGTTCAGATCGAA	HHDGHFHHHHHFH@B?HGHCHHHHE:HHFFHEHHFH	RG:Z:s_8_sequence.txt.gz	IH:i:0	NH:i:0	YU:Z:unmapped

I`m getting the following error. Though the reads are paired-end, the program does not recognize it as paired end. How do I get the program to run? If I dont specify any parameter (not use --pair=yes), it gives me an output with all 0 counts.

  File "dexseq_count.py", line 132, in <module>
    for af, ar in HTSeq.pair_SAM_alignments( HTSeq.SAM_Reader( sam_file ) ):
  File "/usr/lib64/python2.6/site-packages/HTSeq-0.5.4p3-py2.6-linux-x86_64.egg/HTSeq/__init__.py", line 612, in pair_SAM_alignments
    raise ValueError, "'pair_alignments' needs a sequence of paired-end alignments"
ValueError: 'pair_alignments' needs a sequence of paired-end alignments

[dpryan]

None of your reads are mapped as pair-end (at least of the reads you used in your example). Why you're still not getting any counts when not specifying that you have paired-end reads I don't know. Can you post the exact command that you're using?

[alpesh]

python dexseq_count.py   zea_mays.AGPv2.62.gff sorted_samfile.sam exon_counts.txt

Here is the command I used, all the exons (for 30k genes) come up with a 0 number in the output if nothing is specified about paired-e

top of output file

AC147602.5_FG004:001    0
AC147602.5_FG004:002    0
AC147602.5_FG004:003    0
AC147602.5_FG004:004    0
AC147602.5_FG004:005    0
AC148152.3_FG001:001    0
AC148152.3_FG001:002    0
AC148152.3_FG001:003    0
AC148152.3_FG001:004    0
AC148152.3_FG002:001    0

[dpryan]

Well, I don't know about the AGPv2.62 version, but at least in the AGPv3.18 available from ensembl there are no chromosomes/contigs with names like chr1, chr2, etc. That could certainly result in 0 counts for everything (though probably some warnings too). Perhaps try opening the coordinate-sorted bam file in IGV or something similar and see if there's any obvious visual reason to get 0 counts.

[alpesh]

hi dpryan, i have to use AGPv2.62 annotation,,,the my gtf file has chr1,chr2 etc., when you say none of the reads are paired end, it is because of the column 2 flags being 16 (reverse strand), 0(forward strand) and 4(unmapped) ?

[alpesh]

let me give an example.

A couple of lines from my gtf file shows coordinates of a gene and its first exon

chr1	dexseq_prepare_annotation.py	aggregate_gene	300422454	300435350	.	+	.	gene_id "GRMZM2G077596"
chr1	dexseq_prepare_annotation.py	exonic_part	300422454	300422756	.	+	.	transcripts "GRMZM2G077596_T01"; exonic_part_number "001"; gene_id "GRMZM2G077596"

If i want to view all reads mapping to the first exon, i can use samtools

samtools view input.bam chr1:300422454-300422756

Any help will be greatly appreciated


this is the output for the previous command

GALZUI2_0001:2:103:1190:211#0/1	0	chr1	300422484	0	36M	*	0	0	CTTCTTTTGTTCTTTAATTTGGTTCGTACGTACAAG	HHHHFEHCCHCCHHHHHGHHG<BEGHCFHHHHHCHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:6:220:1972#0/1	0	chr1	300422515	0	36M	*	0	0	ACAAGACTTCTCGGATCACTCGTCTTCTTTGATTGC	HHHHHHHHHFHHHHHHHHHHHHHHHHGHHHHHHHHG	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:42:1567:1468#0/1	0	chr1	300422526	0	36M	*	0	0	CGGATCACTCGTCTTCTTTGATTGCATCATCGAGAC	HHHHHHHHHHIHHHHHHHHHHHHHHGHHHHHHHHEH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:120:1465:1034#0/1	0	chr1	300422541	0	36M	*	0	0	CTTTGATTGCATCATCGAGACCTGCATTTTCCCTTC	CDCCC;GDGG;GGGGGG7G<GGGGGGGGGGGGGGGG	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:11:502:602#0/1	0	chr1	300422554	0	36M	*	0	0	ATCGAGACCTGCATTTTCCCTTCCAAATTCGTCACT	HHHFHHHHHFHHFHHHHHHHHHDHHHEEHHCEHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:99:1503:859#0/1	16	chr1	300422569	0	36M	*	0	0	TTCCCTTCCAAATTCGTCACTCACTCTGGTTGGCCG	FHHGHCHDGHHHGHCHGHGHHHHHEHHHHHBGGGBG	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:118:626:857#0/1	16	chr1	300422569	0	36M	*	0	0	TTCCCTTCCAAATTCGTCACTCACTCTGGTTGGCCG	H?DDHH<GHHGHHHHD;HEHHDHHHGHHHHGHHDHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:59:1772:1903#0/1	0	chr1	300422580	0	36M	*	0	0	ATTCGTCACTCACTCTGGTTGGCCGCCTTCTGTCTT	FHHHHHHGHHHDHHHHHDHHHHHHEHHHHHHHGHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:75:95:1416#0/1	16	chr1	300422586	0	1S35M	*	0	0	ACACTCACTCTGGTTGGCCGCCTTATGTCTTCTGAT	##########B?288<10*7=?..'7?C3CBD?DHF	MD:Z:23X11	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:18:1001:1651#0/1	0	chr1	300422587	0	36M	*	0	0	ACTCACTCTGGTTGGCCGCCTTCTGTCTTCTGATCC	HHHHHHHGHHHHHGEHHFHHHHHHHHHHHHHHHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:54:199:1717#0/1	16	chr1	300422600	0	36M	*	0	0	GGCCGCCTTCTGTCTTCTGATCCAATCCGGTTGAAA	DHHFHIHHHHHHEHHHGHHDHHHFHHHHHDHHHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:27:889:358#0/1	16	chr1	300422647	0	1S35M	*	0	0	TCTTCCAGCAAGATCTGGCACATAAGGAGAATCGGC	GHHH=HHHHHHHHFH=HHFEHHHHHHHGHHHHHHHC	MD:Z:35	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:37:242:1709#0/1	16	chr1	300422679	0	36M	*	0	0	GGCAAGAACCATTCTGCAAATGAGGCCGGATACGCG	HFHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:78:1327:822#0/1	16	chr1	300422679	0	36M	*	0	0	GGCAAGAACCATTCTGCAAATGAGGCCGGATACGCG	HHHHHHHFHGHHHHFHHHGHHHHHHHHHHHHHHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:106:745:1364#0/1	16	chr1	300422680	0	1S35M	*	0	0	TGCAAGAACCATTCTGCAAATGAGGCCGGATACGCG	HHHHHHHEHHHHH8HHHHHHHBHHHHHEGHIHIGHH	MD:Z:35	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:112:510:330#0/1	16	chr1	300422712	0	36M	*	0	0	GCGGCTTGAATCGGCGGTGTTCCAGCTCACCCCGAC	HHHGHIGFHIHFHGHIHHHHGHEHHHGEHGHHHHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1
GALZUI2_0001:2:76:91:1422#0/1	0	chr1	300422734	0	23M357N13M	*	0	0	CAGCTCACCCCGACCCGCACCAGGTGTGATTTAGTT	HHHHHHHGIHHGHGHGHHHHHBHH=HHFEHHHEHHH	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1	YS:A:+
GALZUI2_0001:2:36:34:147#0/1	0	chr1	300422741	0	16M357N20M	*	0	0	CCCCGACCCGCACCAGGTGTGATTTAGTTGTGGTGG	HHHHHGHHHHHHHIHHHHHHHHIHHHHHHHHHHHHG	MD:Z:36	RG:Z:s_2_sequence.txt.gz	IH:i:1	NH:i:1	YS:A:+

But in the output from

python dexseq_count.py zea_mays.AGPv2.62_mod.gff sorted_sam.sam counts_exons.txt

and then searching for the gene gives

grep GRMZM2G077596 counts_exons.txt

GRMZM2G077596:001       0
GRMZM2G077596:002       0
GRMZM2G077596:003       0
GRMZM2G077596:004       0
GRMZM2G077596:005       0
GRMZM2G077596:006       0
GRMZM2G077596:007       0
GRMZM2G077596:008       0
GRMZM2G077596:009       0
GRMZM2G077596:010       0
GRMZM2G077596:011       0
GRMZM2G077596:012       0
GRMZM2G077596:013       0

[Simon Anders]

All the alignments in your SAM file excerpt have an alignment quality (5th column) of zero but, by default, dexseq-count.py only counts read with an alignment quality of at least 10. Try to find out why they are all zero, and if this is just a bogus output of your aligner, use the option '-a 0' to set the minimum quality to 0.