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Recent Replies
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
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Thank you for your response.
Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
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In the meantime there is also
seqtk gc
https://github.com/lh3/seqtk
seqtk gc
Usage: seqtk gc [options] <in.fa>
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I have employed your above suggested approach for BQSR (latter one).
I will try former approach too (that does not require reference vcf fi…
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Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
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This is not how HPCs work. Things do not happen automatically and independent of the job scheduler.
If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP
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Using [**EntrezDirect**][1] you can find the location of this SNP:
$ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples
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For variant calling I followed following steps:
**Step 1**
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You can specify conda environments and containers directly in the modules, see for example:
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> ~/Downloads/uniprot_sprot.dat
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Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based).
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I'm having this exact same problem. PolyA RNA-Seq library, running with --fr in hisat2 gives a high fraction of concordant single-mappers, …
Comment: How to create a mutation frequency comparison plot?
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That's awesome thank you. Found out after a bit of researching that this is called a `Cleveland Dot Plot` if anyone else comes across this.
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Demultiplexing is typically done using Illumina software? Have you done this already?: https://www.10xgenomics.com/support/software/cell-ra…
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If you simply want to merge "technical" sequencing replicates then you can do the following
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