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Would it be possible to export FASTA from the command line version? Web based version supports exporting a FASTA but having a command line version to do that as well would be a nice addition.
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Hi,
I got results of the MergeUMIs10x.py, which consisted of .matched_reads.txt, .merged.fasta, .merged.subreads.fastq and .UMI_only.fasta. What is the difference between .UMI_only.fasta and .merged.…
ssscj updated
3 years ago
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['F:\\Sara\\fragpipe\\jre\\bin\\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx20G', WindowsPath('F:/Sara/fragpipe/tools/MSFragger-4.1/MSFragger-4.1.jar'), '--generate_expect_functions', 'DQB2-notry…
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Hello!
Ragtag is a great software, I am a newbie and I have two small questions.
The first one is, "ref1.fasta" and "ref2.fasta" in `ragtag.py scaffold -o out_1 ref1.fasta query.fasta
ragtag.py…
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When using `jruby-9.1.8.0@parse_fasta` gemset, the tests are flaky and randomly failing. When using MRI ruby the tests always pass though.
I ran the rspec suite a couple of times like this
```
…
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Dear METABOLIC support team,
I now don't have the problem with the conda environment, indicated from the error and log file. For the reason, I don't know, as I didn't change anything with the modul…
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In particular:
> Converting FASTQ to FASTA
> Remove ambits...
> Rename and trim
> Processing 16SA_R1.trim.fasta and 16SA_R2.trim.fasta
> Processing 16S_R1.trim.fasta and 16S_R2.trim.fasta
> Files Nam…
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Hello,
So i m trying to run genome-guided Trinity. I produced the bam file from STAR and run the following command
Trinity --genome_guided_bam PRJNA481226.Aligned.sortedByCoord.out.bam --CPU 14 -…
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I want to generate a db of all kmers and their counts for a reference genome using `meryl count`, then for thousands of small (~1-5 kbp) sequences I want to extract all kmers and find their counts in …