Moderator: Ian
Ian ♦ 5.5k
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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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... 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 7 days ago by
Ian ♦ 5.5k
0
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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 4 months ago by
Ian ♦ 5.5k
0
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1
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435
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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 7 months ago by
Ian ♦ 5.5k
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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 9 months ago by
Ian ♦ 5.5k
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2
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702
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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
...
written 9 months ago by
Ian ♦ 5.5k
1
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3
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550
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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 10 months ago by
Ian ♦ 5.5k
1
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1
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... When you run htseq-count check that the -i flag is set to ID (-i ID) and not 'gene_id', which is the GTF default. ...
written 10 months ago by
Ian ♦ 5.5k
0
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1
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... You could try SNPRelate (https://bioconductor.org/packages/release/bioc/html/SNPRelate.html). You can create a PCA plot of the samples based on their VCF files. ...
written 10 months ago by
Ian ♦ 5.5k
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... Seqminer (https://sourceforge.net/projects/seqminer/) is old (2012), but allows you to download the genes from the different clusters you observe, something I have not managed to do with Deeptools. ...
written 10 months ago by
Ian ♦ 5.5k
2
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730
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... Thanks to the other contributors, but unfortunately the EMBL format created was not accepted by ENA. However, I have found [EMBLmyGFF3][1], which will create a valid file.
The validation program can be found [HERE][2].
BED to GFF3 used [THIS][3].
[1]: https://github.com/NBISweden/EMBLmyGFF3 ...
written 15 months ago by
Ian ♦ 5.5k
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For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
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For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
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