Simon Anders posted a comment on ticket #35

Hi Katy the SourceForge page is dead since years. Please repost your support request on GitHub: https://github.com/simon-anders/htseq/issues Simon

katy adler created ticket #35

htseq count problem

Simon Anders committed [r281]

last commit to Sourceforge SVN; new repo is htt...

Ariel Paulson created ticket #5

htseq-count: option to count all alignments.

Adam Rivers created ticket #34

BAM and SAM readers cannot parse "=" in CIGAR format

Alva Rani James created ticket #33

Htseq throws error for exonic read counts

Paul Theodor Pyl committed [r280]

Implemented new functions in BAM_Reader and BAM...

Paul Theodor Pyl committed [r279]

Modified version checking behaviour to work pro...

Zach created ticket #32

HTSeq count txt file first line empty

Simon Anders committed [r278]

Simon Anders committed [r277]

updates to documentation

Anonymous modified a comment on ticket #1

status: open --> closed

Simon Anders posted a comment on ticket #31

No, because htseq-count is specifically designed for differential-expression calling,...

Gayle McEwen created ticket #31

Paired end reads, bacterial genome

Simon Anders committed [r276]

tagging 0.6.1p1

Simon Anders committed [r275]

fixed wrong version number in _version.py

Simon Anders committed [r274]

tagging release 0.6.1

amuller created ticket #30

Counts on single and paired ends reads merged bam file

Simon Anders committed [r273]

one more question added to htseq-count FAQ

Simon Anders committed [r272]

minor formatting in docs

Simon Anders committed [r271]

version 0.6.1

Simon Anders committed [r270]

- added BED parser

Simon Anders committed [r269]

added otherparsers.rst, which was missing in pr...

Simon Anders committed [r268]

moved VCF docu to otherparsers.rst

Simon Anders committed [r267]

added GenomicArrayOfSets.svg, which was missing...

Simon Anders committed [r266]

version 0.6.0

Simon Anders committed [r265]

finished improved htseq-count and updated docum...

Simon Anders committed [r264]

count2 now works and is tested

Paul Theodor Pyl committed [r263]

Fixed wiggle parser and some weird syntax error...

Paul Theodor Pyl committed [r262]

WIG_Reader initial draft

Simon Anders committed [r261]

fized some more nonsense pair_SAM_alignments_wi...

Simon Anders committed [r260]

added 'pair_SAM_alignments_with_buffer', not ye...

JahnDavik posted a comment on ticket #29

Dear Simon, If I interpret you correctly, than this is not a problem that HTSeq would...

Simon Anders posted a comment on ticket #29

If you have aligned to a transcriptome, the each gene is a different reference sequence,...

Simon Anders posted a comment on ticket #28

Sorry, I can't follow your question. It sounds as if you are following some instructions...

Yaron de Leeuw created ticket #4

UMI Support in htseq-count ( Patch included)

JahnDavik created ticket #29

making the count matrix from a fasta reference

Jian Wang created ticket #28

htseq counting problem

Simon Anders committed [r259]