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Recent Replies
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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Pierre Lindenbaum
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> server so I cannot use Blat for this purpose.
blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴
150
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`.
It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
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Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
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Hagen
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thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with
…
Comment: Per base sequence content failed miserably
by
Kai Xin
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0
will look into that. Thank you very much
Comment: Korean human genome reference file
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SeoGyun
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0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
•
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thank you for your reply
https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md
i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
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cmdcolin
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Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: Removing duplicates
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joe
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I'd try those OP @samuel recommends
My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
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swbarnes2
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No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do:
bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option.
Get the PDB ID's
$ ./get.sh "Mus musculus" AHR
4M4X
5NJ8
5V0L
8H77
Then use `curl` to g…
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