HTSeq
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Overview
Installation
A tour through HTSeq
Tutorials
Counting reads
Reference API
Sequences and FASTA/FASTQ files
Positions, intervals and arrays
Read alignments
Features
Other parsers
Miscellaneous
htseq-count
: counting reads within features
htseq-count-barcodes
: counting reads with cell barcodes and UMIs
Quality Assessment with
htseq-qa
Version history
Contributing
HTSeq
Index
Edit on GitHub
Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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V
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W
Symbols
--a
htseq-count command line option
--add-chromosome-info
htseq-count command line option
--additional-attr
htseq-count command line option
--counts-output-sparse
htseq-count command line option
--counts_output
htseq-count command line option
--feature-query
htseq-count command line option
--format
htseq-count command line option
--gamma
htseq-qa command line option
--help
htseq-count command line option
htseq-qa command line option
--idattr
htseq-count command line option
--max-reads-in-buffer
htseq-count command line option
--maxqual
htseq-qa command line option
--mode
htseq-count command line option
--nonunique
htseq-count command line option
--nosplit
htseq-qa command line option
--nprocesses
htseq-count command line option
--order
htseq-count command line option
--outfile
htseq-qa command line option
--quiet
htseq-count command line option
--readlength
htseq-qa command line option
--samout
htseq-count command line option
--samout-format
htseq-count command line option
--secondary-alignments
htseq-count command line option
--stranded
htseq-count command line option
--supplementary-alignments
htseq-count command line option
--type
htseq-count command line option
htseq-qa command line option
--version
htseq-count command line option
-a
htseq-count command line option
-c
htseq-count command line option
-f
htseq-count command line option
-g
htseq-qa command line option
-h
htseq-count command line option
htseq-qa command line option
-i
htseq-count command line option
-m
htseq-count command line option
htseq-qa command line option
-n
htseq-count command line option
htseq-qa command line option
-o
htseq-count command line option
htseq-qa command line option
-p
htseq-count command line option
-q
htseq-count command line option
-r
htseq-count command line option
htseq-qa command line option
-s
htseq-count command line option
-t
htseq-count command line option
htseq-qa command line option
_
__version__ (in module HTSeq)
A
add_chrom() (HTSeq.GenomicArray method)
aligned (HTSeq.Alignment attribute)
Alignment (class in HTSeq)
AlignmentWithSequenceReversal (class in HTSeq)
alt (HTSeq.VariantCall attribute)
apply() (HTSeq.ChromVector method)
aQual (HTSeq.SAM_Alignment attribute)
attr (HTSeq.GenomicFeature attribute)
auto_add_chroms (HTSeq.GenomicArray attribute)
B
BAM_Reader (class in HTSeq)
BED_Reader (class in HTSeq)
BigWig_Reader (class in HTSeq)
BowtieAlignment (class in HTSeq)
BowtieReader (class in HTSeq)
bundle_multiple_alignments() (in module HTSeq)
C
check() (HTSeq.CigarOperation method)
chrom (HTSeq.GenomicInterval attribute)
(HTSeq.VariantCall attribute)
chrom_vectors (HTSeq.GenomicArray attribute)
chroms() (HTSeq.BigWig_Reader method)
cigar (HTSeq.SAM_Alignment attribute)
CigarOperation (class in HTSeq)
contains() (HTSeq.GenomicInterval method)
D
descr (HTSeq.Sequence attribute)
E
end (HTSeq.GenomicInterval attribute)
end_as_pos (HTSeq.GenomicInterval attribute)
end_d (HTSeq.GenomicInterval attribute)
end_d_as_pos (HTSeq.GenomicInterval attribute)
extend_to_include() (HTSeq.GenomicInterval method)
F
failed_platform_qc (HTSeq.SAM_Alignment attribute)
FastaReader (class in HTSeq)
FastqReader (class in HTSeq)
FileOrSequence (class in HTSeq)
filter (HTSeq.VariantCall attribute)
format (HTSeq.VariantCall attribute)
fos (HTSeq.FileOrSequence attribute)
frame (HTSeq.GenomicFeature attribute)
from_bedgraph_file() (HTSeq.GenomicArray method)
from_bigwig_file() (HTSeq.GenomicArray method)
G
GenomicArray (class in HTSeq)
GenomicArrayOfSets (class in HTSeq)
GenomicFeature (class in HTSeq)
GenomicInterval (class in HTSeq)
GenomicInterval_from_directional() (in module HTSeq)
GenomicPosition (class in HTSeq)
get_gff_line() (HTSeq.GenomicFeature method)
get_line_number_string() (HTSeq.FileOrSequence method)
get_reverse_complement() (HTSeq.Sequence method)
get_sam_line() (HTSeq.SAM_Alignment method)
GFF_Reader (class in HTSeq)
H
htseq-count command line option
--a
--add-chromosome-info
--additional-attr
--counts-output-sparse
--counts_output
--feature-query
--format
--help
--idattr
--max-reads-in-buffer
--mode
--nonunique
--nprocesses
--order
--quiet
--samout
--samout-format
--secondary-alignments
--stranded
--supplementary-alignments
--type
--version
-a
-c
-f
-h
-i
-m
-n
-o
-p
-q
-r
-s
-t
htseq-qa command line option
--gamma
--help
--maxqual
--nosplit
--outfile
--readlength
--type
-g
-h
-m
-n
-o
-r
-t
I
id (HTSeq.VariantCall attribute)
inferred_insert_size (HTSeq.SAM_Alignment attribute)
info (HTSeq.VariantCall attribute)
interval (HTSeq.GenomicFeature attribute)
intervals() (in module HTSeq)
is_contained_in() (HTSeq.GenomicInterval method)
iv (HTSeq.Alignment attribute)
L
length (HTSeq.GenomicInterval attribute)
line_no (HTSeq.FileOrSequence attribute)
M
make_feature_genomicarrayofsets() (in module HTSeq)
mate_aligned (HTSeq.SAM_Alignment attribute)
mate_start (HTSeq.SAM_Alignment attribute)
metadata (HTSeq.GFF_Reader attribute)
(HTSeq.VCF_Reader attribute)
N
name (HTSeq.GenomicFeature attribute)
(HTSeq.Sequence attribute)
nomatch_code (HTSeq.SolexaExportAlignment attribute)
not_primary_alignment (HTSeq.SAM_Alignment attribute)
O
optional_field (HTSeq.SAM_Alignment attribute)
optional_fields (HTSeq.SAM_Alignment attribute)
overlaps() (HTSeq.GenomicInterval method)
P
pair_SAM_alignments() (in module HTSeq)
pair_SAM_alignments_with_buffer() (in module HTSeq)
paired_end (HTSeq.Alignment attribute)
parse_GFF_attribute_string() (in module HTSeq)
passed_filter (HTSeq.SolexaExportAlignment attribute)
pcr_or_optical_duplicate (HTSeq.SAM_Alignment attribute)
pe_which (HTSeq.SAM_Alignment attribute)
pos (HTSeq.VariantCall attribute)
(in module HTSeq)
proper_pair (HTSeq.SAM_Alignment attribute)
Q
qual (HTSeq.SequenceWithQuality attribute)
(HTSeq.VariantCall attribute)
qualstr (HTSeq.SequenceWithQuality attribute)
query_from (HTSeq.CigarOperation attribute)
query_to (HTSeq.CigarOperation attribute)
R
range() (HTSeq.GenomicInterval method)
range_d() (HTSeq.GenomicInterval method)
read (HTSeq.Alignment attribute)
read_as_aligned (HTSeq.AlignmentWithSequenceReversal attribute)
read_as_sequenced (HTSeq.AlignmentWithSequenceReversal attribute)
ref (HTSeq.VariantCall attribute)
ref_iv (HTSeq.CigarOperation attribute)
reserved (HTSeq.BowtieAlignment attribute)
S
SAM_Alignment (class in HTSeq)
samples (HTSeq.VariantCall attribute)
score (HTSeq.GenomicFeature attribute)
seq (HTSeq.Sequence attribute)
Sequence (class in HTSeq)
SequenceWithQualities (class in HTSeq)
size (HTSeq.CigarOperation attribute)
SolexaExportAlignment (class in HTSeq)
SolexaExportReader (class in HTSeq)
source (HTSeq.GenomicFeature attribute)
start (HTSeq.GenomicInterval attribute)
start_as_pos (HTSeq.GenomicInterval attribute)
start_d (HTSeq.GenomicInterval attribute)
start_d_as_pos (HTSeq.GenomicInterval attribute)
steps() (HTSeq.ChromVector method)
(HTSeq.GenomicArray method)
strand (HTSeq.GenomicInterval attribute)
stranded (HTSeq.GenomicArray attribute)
substitutions (HTSeq.BowtieAlignment attribute)
supplementary (HTSeq.SAM_Alignment attribute)
T
trim_left_end() (HTSeq.Sequence method)
trim_left_end_with_quals() (HTSeq.SequenceWithQualities method)
trim_right_end() (HTSeq.Sequence method)
trim_right_end_with_quals() (HTSeq.SequenceWithQualities method)
type (HTSeq.CigarOperation attribute)
(HTSeq.GenomicFeature attribute)
typecode (HTSeq.GenomicArray attribute)
V
VariantCall (class in HTSeq)
VariantCall.unpack_info() (in module HTSeq)
VCF_Reader (class in HTSeq)
VCF_Reader.make_info_dict() (in module HTSeq)
VCF_Reader.parse_meta() (in module HTSeq)
W
WiggleReader (class in HTSeq)
write_bedgraph_file() (HTSeq.GenomicArray method)
write_bigwig_file() (HTSeq.GenomicArray method)
write_to_fastq_file() (HTSeq.SequenceWithQuality method)
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