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Any plans on adding CIGAR strings to SAM output so I can load the alignments in a genome browser?
_Originally posted by @yhoogstrate in https://github.com/vpc-ccg/circminer/issues/4#issuecomment-64…
fhach updated
4 years ago
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I am having an issue with the output from using --quantMode TranscriptomeSAM missing mapped reads relative to the same reads mapped to the corresponding genome. And there is a issue(#315 launch by gho…
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I try to use CONDA environment and manually install pasa, but in the manual installation, because it is a non root user, the software that pasa depends on is installed with CONDA, only the pasa softwa…
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I think hisat is not handling ribosomal RNA reads very well (see image). Neither are Star or Tophat2.
Tophat also finds a bunch of strange splice junctions (top)
Hisat is finding a bunch of splice jun…
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I am running STAR and StringTie on RNAseq data from 4 samples (PE 100bp, 60M reads/sample, stranded) and am looking at the merged.stats file. The numbers for novel stuff being found in my samples is R…
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Hello,
I am currently trying to use SIDR to detect contaminants in a few cnidarian genomes I am working with. From reading the publication for this program I assumed there would be a way to use two…
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Hello, everyone
I used the PASA (v2.5.3) pipeline to update the annotations from EVM with the following command: `/vol2/YL_group/YL/software/PASApipeline-master/Launch_PASA_pipeline.pl -c alignAssemb…
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Hi, I have some samfiles which are output of minimap2 used for long nanopore reads (RNA seq). Because minimap does not have the tag XS, I added it manually to each read.
However stringtie continue to…
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Hi Phil,
I was wondering if you could add Rail-RNA to MultiQC. Below is the requested info:
* **Name of tool:**
* Rail-RNA
* **Tool description:**
* Rail-RNA is a spliced alignment pr…
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Dear Alex;
I am performing RNA sequence analysis to determine the DE genes in a human cell line sequenced with Ion Proton. I am using the default STAR settings and I get a low percentage of uniquel…