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I am running bam-readcount as part of an analysis of three samples. The first two finished in a few hours but the third has been running for 40h (with 100% use of one CPU) already.
`/usr/bin/bam-re…
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Hi,
The estimated genome size of the coastal redwood output by GenomeScope is 27.0 Gbp and 2.293 Gbp for Gossypium barbadense in this paper . But I'm confused about how to get these results from http…
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this is
this is the error code when reaching the multifastq, this is the same pipeline as #1021
I removed some entries to make it readable.
take note the version of my snakePipes
```bash
$snak…
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Hi, dear friends. I have a question on processing rawdata. When I made PCA or Dst. analyses, I need to take a outgroup species as reference genome for processing rawdata. My question is that whether t…
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Tophat 2.1.1 was not compatible with bowtie2 v2.3 in our server. To get tophat to work, I had to switch to bowtie2 v2.2.9.
I was getting this error message with bowtie2 v2.3
--------------------…
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Add more columns to data_clinical.txt, using http://oncotree.mskcc.org/cdd/api/ to standardize column names if possible.
- [ ] `MOUSE_CONTAMINATION` - For batches with at least 1 PDX sample, report…
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Hi,
Thank you for this great and simple tool!
I'm working with non-human data that which we have found many TAD callers seem to have a high false positive rate on - judging from how it adds up …
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Hi.
When I performed a de novo assembly using HIFI, I obtained a genome size of 1.7 Gb. Since there was no prior information available about my sample, I decided to estimate the genome size. When …
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Hi rMATS team,
I wanted to discuss a discrepancy I've encountered between the results obtained from rMATS-turbo analysis and what I observed in the Integrated Genome Viewer (IGV) while examining RNA-…
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Hi,
I'm trying to generate a library from scratch based on GRCh38 with some regions masked (GRC exclusions). Very early in the main script, the reference genome FASTA is copied to a file with the m…