Moderator: Ian
Ian ♦ 5.6k
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- University of Manchester, UK
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- IanDcalling
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Member of the Faculty of Life Science's bioinformatics core facility.
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http://www.youtube.com/user/ManchesterBCF/videos?view=1&flow=grid for video tutorials.
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I specialise in ChIP-seq analysis, but also run RNA-seq and other NGS applications. Data comes, almost exclusively from illumina sequencers, but I used to mostly analyse SOLiD sequence.
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I am interested in the analysis, organisation and presentation of genomics data. I have a special place in my heart for the hunting of transcription factor binding sites.
Posts by Ian
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... Hi I used to use the ECR browser for this type of question, you can find the details at https://ecrbase.dcode.org/. Just be aware that it was last updated in 2008! But this might be useful to you. ...
written 3 months ago by
Ian ♦ 5.6k
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... Funnily enough I had looked at it because it mentioned the use of MFA files. Unfortunately it assumes that every sequence in the file is a different species, and is a multiple alignment. Whereas my file has a many pair-wise alignments. I rerun MAUVE and the .alignment file is an almost identical ...
written 8 months ago by
Ian ♦ 5.6k
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... Thanks. I have given Mauve a try, but I didn't get a close to what I wanted with WGvista. ...
written 8 months ago by
Ian ♦ 5.6k
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... Hello.
I have aligned the 88 contigs of an *E.coli* *de novo* assembly against the closest reference genome, using WGvista. The aim is to identify structural differences in the alignment, in detail. The output of WGvista is a multiple fasta alignment (MFA) file. The format gives pairwise alignm ...
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... The following text is from UCSC's page on PhastCons / PhyloP ([LINK][1]). I think for the size of splice-sites that the fine grained PhyloP score might be most useful.
> "PhastCons is a hidden Markov model-based method that estimates the
> probability that each nucleotide belongs to a conser ...
written 9 months ago by
Ian ♦ 5.6k
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... The suggestion of using --SPMR goes against the author's own recommendations:
https://github.com/taoliu/MACS/wiki/Call-differential-binding-events ...
written 13 months ago by
Ian ♦ 5.6k
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... If in any doubt just rerun 'samtools sort'. Remember if you have multiple processors then use '-@ N', where N is the number of processor cores. ...
written 17 months ago by
Ian ♦ 5.6k
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... If you are making copies of a file, particularly if the copy is going to be downloaded off a server, then using `md5sum` will produce a hash (string of characters) that are unique to the file, and can be matched with the copy. ...
written 19 months ago by
Ian ♦ 5.6k
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... It is now possible to view this type of data as a custom track on the UCSC Browser:
http://genome.ucsc.edu/goldenPath/help/interact.html
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written 19 months ago by
Ian ♦ 5.6k
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... I have tackled this on a small scale by retaining SAM reads used by htseq-count (--samout), and removing those excluded from the final counts, using sed '/XF:Z:$/d;/XF:Z:__/d'.
After normalisation by DESeq2 I use the scaleFactor to scale the SAM > BAM files, using bedtools genomecov (-scale).
...
written 19 months ago by
Ian ♦ 5.6k
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For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
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