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Hello!
I am trying to analyse differential gene expression in 83 samples split up into three groups following the protocol described by Pertea et al., 2016 (doi:10.1038/nprot.2016.095).
Now I h…
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Hello again!
I'm trying to output results in sam or bam format, but the command results in a bam file which when converted contains only headers, with no sequence. Stopping mirge early shows that s…
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Hi,
Thanks for this user friendly R package.
I'm starting to play around with snapcount, I would like to know what's your advice for querying with many intervals spanning many genes across a full…
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Hello,
MACS2 stalls at the following line:
```
#3 Pre-compute pvalue-qvalue table...
```
I have two BAM files, one converted to BAM from Bowtie2 output and the other which has underwent some proces…
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Hello htslib devs,
I'm starting to work on a htsget-server implementation that relies on htslib, based on preliminary work on https://github.com/samtools/hts-specs/pull/385. The first issue I've fo…
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Hi @marcus1487, I was using remora API on real direct RNA-seq data, but ran into errors from this command:
```python
io_read = Read.from_pod5_and_alignment(
pod5_read_record=pod5_reads[ba…
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Is the STAR aligner `/path/to/STAR-2.7.0f/bin`? Thank you.
_Originally posted by @cmccabe0728 in https://github.com/STAR-Fusion/STAR-Fusion/issues/305#issuecomment-1069550291_
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Dear,
I succeeded a very similar first run with docker (ONT assembly all the rest the same). The ONT run ended after few hours and gave results.
The second run hangs on some prothint record (Pac…
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`samtools mpileup -r chrA:nnn-mmm` includes region `chrA:nnn-mmm` correctly, but for some combinations of BAM files it also returns pileups from the same coordinates on other contigs, for example `chr…
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Hello,
I have some questions about functions within the software and mainly I am seeking some advice on parameter setting as I believe the developers might have a better idea of how to tackle this …