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Im getting a error I haven't come across before.
Any Ideas?
sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa
Checking required depe…
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_Guillermo Parada from Sanger reported on 1 Feb 2016:_
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I writing to you to kindly inform that dexseq_count.py is currently incompatible with the SAM output of STAR (probably the most widely use…
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Hi Brad,
My bcbio run has been unable to proceed past a certain T-N paired sample at the prioritisation step, up to the generation of the manta tsv files. I checked the commands and can't find anyt…
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Hi,
I successfully build piranha with bamtools. When i attempt to run the software with my bam files I receive the following error:
`ERROR: Responses cannot be provided in BAM format if they are n…
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Should this tool be deprecated in favor of https://github.com/galaxyproject/tools-iuc/blob/master/tools/htseq_count/htseq-count.xml
https://github.com/galaxyproject/tools-iuc/tree/master/tools/htse…
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Add option `--split-id SEPARATOR`:
- split and expand gene list values by the supplied separator if `-g` option is used
- default `None` means no splitting
- problem/use case: cufflinks creates merged…
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Would be great to have a module to parse logs from [`htseq-count`](http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Suggested by @jcgrenier in #311
ewels updated
7 years ago
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_Adam Tebbe wrote:_
Hello Simon,
I was trying out your HTSeq library (installed version 0.6.1 from the public pypi repository). I am specifically trying out the htseq-qa script and have found that …
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I am running anaconda ->Python 2.7.11 :: Anaconda 2.5.0 (64-bit)
I installed htseq and pysam as as
conda install -c bioconda pysam
conda install -c bioconda htseq
my input file alignment.bam is a b…
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I recently upgraded to Pysam v. 0.9.0 and now HTSeq fails to correctly search for alignments within a genomicInterval from a BAM_Reader object.
Here's the error code and an example.
```
inbam = HTS…