Moderator: Ian
Ian ♦ 5.3k
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- University of Manchester, UK
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- http://personalpages.m...
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- IanDcalling
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- Joined:
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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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... 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 3 months ago by
Ian ♦ 5.3k
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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 5 months ago by
Ian ♦ 5.3k
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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 5 months ago by
Ian ♦ 5.3k
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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 5 months ago by
Ian ♦ 5.3k
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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 6 months ago by
Ian ♦ 5.3k
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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 6 months ago by
Ian ♦ 5.3k
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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 6 months ago by
Ian ♦ 5.3k
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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 11 months ago by
Ian ♦ 5.3k
5
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... Does anyone have a method for creating an EMBL-flatfile from a FASTA file of sequence, and a BED file of genes and repeats?
The purpose is for submission of an annotate genome to the ENA.
Thanks. ...
written 12 months ago by
Ian ♦ 5.3k
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... There might still be useful results in experiment 2, but Pvalue and fold change are only indicative at best. The results might give you leads for further lab experiments, or be impressive enough to warrant a second attempt with replication. ...
written 13 months ago by
Ian ♦ 5.3k
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For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
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For How to add gene annotation to a UCSC assembly hub?
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For Should the reads of biological replicates be combined for ChIP-seq peak calling?
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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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14 months ago,
created an answer that has been accepted.
For A: How to add gene annotation to a UCSC assembly hub?
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14 months ago,
created a question with more than 10,000 views.
For Meaning Of Samtools 'Vcfutils.Pl Varfilter -Q'?
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16 months ago,
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For A: Download Genomic Ranges From A List Of Coordinates Via Web
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For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
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19 months ago,
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21 months ago,
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For A: Download Genomic Ranges From A List Of Coordinates Via Web
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21 months ago,
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For Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
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