Moderator: Alastair Kerr

gravatar for Alastair Kerr
Alastair Kerr5.2k
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Location:
The University of Edinburgh, UK
Website:
http://bifx1.bio.ed.ac...
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Google Scholar Page
Last seen:
4 days, 7 hours ago
Joined:
7 years ago
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a************@ed.ac.uk
Bioinformatics Core Facility Manager for the Wellcome Trust Centre for Cell Biology in Edinburgh.

Posts by Alastair Kerr

<prev • 266 results • page 1 of 27 • next >
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Answer: A: CoverageBed for RNA-seq strand-specific and paired-end data
... The [Deeptools][1] package is useful for this, specifically the bamCoverage program within it. It has useful documentation using the "--help" flag but I think the "--filterRNAstrand" option will be what you are looking for. [1]: https://deeptools.github.io/ ...
written 15 days ago by Alastair Kerr5.2k
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Answer: A: Error when Asm852v1 (S pombe) genome is installed in ngsplot
... I was looking into this today for a user. I think Asm852v1 is actually H.pylori. ASM294 Should be the correct genome but they only have a download for version 1 and 2 of their program. I've failed so far to alter their code to enable a download from ensembl fungi. If anyone has a pombe tarball fo ...
written 22 days ago by Alastair Kerr5.2k
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Answer: A: Bisulfite sequencing query
... If you already have the sequencing data then I recommend you look at [Bismark][1]. This link will direct you to the software and dependencies was well as a guide to the [QC, trimming & alignment][2]. [1]: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ [2]: http://www.epigenes ...
written 6 months ago by Alastair Kerr5.2k
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Comment: C: Adjusting Peak Calling For Broad Enrichment Of Histone Modifications.
... I removed this script as there now exists a range of decent pack callers.. See [this wikipedia page][1] [1]: https://en.wikipedia.org/wiki/Peak_calling ...
written 7 months ago by Alastair Kerr5.2k
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Comment: C: Check my work? Hyper geometric test on enrichment between iCLIP sites across exp
... Also have a look at the [genometricorr][1] R package. [1]: http://genometricorr.sourceforge.net/ ...
written 10 months ago by Alastair Kerr5.2k
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Comment: C: Needle Crashing on Specific Sequences
... I always use "-sprotein" flag to indicate I am aligning protein sequences when using needle. This should indicate both are proteins and save a few keystrokes. e.g. "needle asequence=seq1.fasta bsequence=seq2.fasta gapopen=3 gapextend=1 outfile=needle.out -sprotein" ...
written 14 months ago by Alastair Kerr5.2k
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Comment: C: generating genome indexes with STAR
... You are still using the tar archive for the fasta files. Use the fasta files extracted from the tar archive ...
written 15 months ago by Alastair Kerr5.2k
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Comment: C: Filtering out the spliced reads from bam file.
... Also look at this [previous thread][1] for some ideas: [1]: https://www.biostars.org/p/89581 ...
written 15 months ago by Alastair Kerr5.2k
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Comment: C: FastQC: GC Content extra peak
... % of reads map? Any of the unmapped reads adapter pairs or primer pairs? If you look at only the reads that map and reads that map to non-repeat regions do you see the same issues? Any sign of bacterial contamination in the unmapped reads? What about over-represented kmers in the report: if foun ...
written 16 months ago by Alastair Kerr5.2k
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Answer: A: How to estimate the power of association test for small sample size
... [G*Power][1] is what I recommend to our researchers for power calculations. Note that you still need a decent understanding of the method but a decent intro can be found on the [wikipedia page][2]. [1]: http://www.gpower.hhu.de/ [2]: https://en.wikipedia.org/wiki/Statistical_power ...
written 17 months ago by Alastair Kerr5.2k

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