usage: htseq-count [options] alignment_file gff_file
This script takes one or more alignment files in SAM/BAM format and a feature
file in GFF format and calculates for each feature the number of reads mapping
to it. See http://htseq.readthedocs.io/en/master/count.html for details.
positional arguments:
samfilenames Path to the SAM/BAM files containing the mapped reads.
If '-' is selected, read from standard input
featuresfilename Path to the file containing the features
optional arguments:
-h, --help show this help message and exit
-f {sam,bam}, --format {sam,bam}
type of <alignment_file> data, either 'sam' or 'bam'
(default: sam)
-r {pos,name}, --order {pos,name}
'pos' or 'name'. Sorting order of <alignment_file>
(default: name). Paired-end sequencing data must be
sorted either by position or by read name, and the
sorting order must be specified. Ignored for single-
end data.
--max-reads-in-buffer MAX_BUFFER_SIZE
When <alignment_file> is paired end sorted by
position, allow only so many reads to stay in memory
until the mates are found (raising this number will
use more memory). Has no effect for single end or
paired end sorted by name
-s {yes,no,reverse}, --stranded {yes,no,reverse}
whether the data is from a strand-specific assay.
Specify 'yes', 'no', or 'reverse' (default: yes).
'reverse' means 'yes' with reversed strand
interpretation
-a MINAQUAL, --minaqual MINAQUAL
skip all reads with alignment quality lower than the
given minimum value (default: 10)
-t FEATURETYPE, --type FEATURETYPE
feature type (3rd column in GFF file) to be used, all
features of other type are ignored (default, suitable
for Ensembl GTF files: exon)
-i IDATTR, --idattr IDATTR
GFF attribute to be used as feature ID (default,
suitable for Ensembl GTF files: gene_id)
--additional-attr ADDITIONAL_ATTR [ADDITIONAL_ATTR ...]
Additional feature attributes (default: none, suitable
for Ensembl GTF files: gene_name)
-m {union,intersection-strict,intersection-nonempty}, --mode {union,intersection-strict,intersection-nonempty}
mode to handle reads overlapping more than one feature
(choices: union, intersection-strict, intersection-
nonempty; default: union)
--nonunique {none,all}
Whether to score reads that are not uniquely aligned
or ambiguously assigned to features
--secondary-alignments {score,ignore}
Whether to score secondary alignments (0x100 flag)
--supplementary-alignments {score,ignore}
Whether to score supplementary alignments (0x800 flag)
-o SAMOUTS [SAMOUTS ...], --samout SAMOUTS [SAMOUTS ...]
write out all SAM alignment records into an output SAM
file called SAMOUT, annotating each line with its
feature assignment (as an optional field with tag
'XF')
-q, --quiet suppress progress report
Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
Public License v3. Part of the 'HTSeq' framework, version 0.10.0.