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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
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Hi there, I'm trying to run doctor.py to check the installation
~/bin/doctor.py
I get this message:
$ ~/bin/doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa …
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If you are using the "get_query_sequences" function from the "pileupcolumn" class, you cannot display the output in the Samtools mpileup format if you select all boolean options to be true.
I thin…
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/bin/bash: bc: command not found
split: invalid number of lines: ?
RuleException:
CalledProcessError in line 104 of /opt/conda/envs/periscope/lib/python3.6/site-packages/periscope/scripts/Snakef…
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The vcf can be used as annotation source for genexus.
Must contain minimal vcf header following specs: https://samtools.github.io/hts-specs/VCFv4.2.pdf
Must contain class and comments from the db
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Hi.
sam output(good feature!) need to be fixed
1, use TAB instead of space.
2, add '@SQ SN:xxx LN:yyy ' into headers
3, modify '@HD VN1.0' to '@HD VN:1.0'
BTW, we can check the output with …
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Duplication is desired? This may be confusing for end users. Both samtools and picard are nearly always installed in locals as the first go-to tool packages.
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Ref ga4gh endpoint here
https://github.com/samtools/hts-specs/pull/530
Rejects the bogus refname provided that we use currently
Have to adjust to not specify any refname, but then it returns …
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Thanks for this very useful workflow. To reduce runtimes, can I suggest adding a 'whitelist' rule to preprocessing? This could reduce runtimes considerably in situations where the targets are limited …
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Pyfasta (written in 2018) is archived, it's successor Pyfaidx isn't suitable for our use (no split function).
However, there is pyfastx (https://github.com/lmdu/pyfastx) which uses samtools index to…