Moderator: Alastair Kerr

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Alastair Kerr5.3k
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Manchester/UK/Cancer Biomarker Centre at CRUK-MI
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https://www.cruk.manch...
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@alastair_kerr
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Posts by Alastair Kerr

<prev • 264 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 3.1 years ago by Alastair Kerr5.3k
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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 3.2 years ago by Alastair Kerr5.3k
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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 3.6 years ago by Alastair Kerr5.3k
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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 3.7 years ago by Alastair Kerr5.3k
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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 4.0 years ago by Alastair Kerr5.3k
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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 4.3 years ago by Alastair Kerr5.3k
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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 4.4 years ago by Alastair Kerr5.3k
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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 4.4 years ago by Alastair Kerr5.3k
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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 4.5 years ago by Alastair Kerr5.3k
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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 4.6 years ago by Alastair Kerr5.3k

Latest awards to Alastair Kerr

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Scholar 5.8 years ago, created an answer that has been accepted. For A: NCBI GI to Gene Description
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Popular Question 6.0 years ago, created a question with more than 1,000 views. For Any Resource For Relative Protein Abundances By Cell Or Organelle?

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