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Search: Posts Made By: malcook
Forum: Bioinformatics 11-24-2017, 11:02 PM
Replies: 2
Views: 1,514
Posted By malcook
wiggletools...

wiggletools (https://github.com/Ensembl/WiggleTools) - you will probably want your bigwigs to be normalized, possibly as made easy with deepTools (https://github.com/deeptools/deepTools)
Forum: Bioinformatics 06-11-2014, 09:33 PM
Replies: 3
Views: 1,577
Posted By malcook
makeTranscriptDbFromBiomart for S. pombe

I just posted an approach to using Biomart at https://www.biostars.org/p/103251/

Here's the nub:


txdb<-makeTranscriptDbFromBiomart(
,biomart ="fungi_mart_22"
...
Forum: Bioinformatics 07-02-2013, 07:42 AM
Replies: 6
Views: 3,971
Posted By malcook
why tss_id and p_id? how to add them? -

The use of tss_id and p_id by cuffdiff is explained (http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output) as
tss_group_exp.diff Primary transcript differential FPKM. Tests differences in the...
Forum: Bioinformatics 05-28-2013, 10:05 PM
Replies: 11
Views: 3,160
Posted By malcook
perl fu bwahaha

assuming all your files are in the contig directory, how about this perl one-liner:

perl -lape '$F[4]+=$o; $F[3]+=$o; $_=join("\t",@F); $m=($m,$F[4])[$m < $F[4]]; $o=$m if eof;' contig/*.gff >...
Forum: Bioinformatics 12-31-2012, 01:38 PM
Replies: 5
Views: 1,411
Posted By malcook
time to learn xargs?

here is a one-liner that uses xargs


basename -a data/rad1/*.dat | xargs -t -I {} bash -c 'cat data/rad1/"{}" data/rad2/"{}" > data/rad3/"{}" ' \;


notes:

this works on my mac/OSX; if...
Forum: Bioinformatics 03-27-2012, 09:01 PM
Replies: 11
Views: 6,881
Posted By malcook
You could find the call to bowtie that tophat...

You could find the call to bowtie that tophat makes and edit it to pass additional parameters taken from an environment variable, say, BowtieExtraTophatOptions

then set BowtieExtraTophatOptions to...
Forum: Bioinformatics 02-10-2012, 07:40 PM
Replies: 2
Views: 1,363
Posted By malcook
http://malcook-gedanken.blogspot.com/2011/06/tabul...

http://malcook-gedanken.blogspot.com/2011/06/tabulating-reads_09.html
Forum: Bioinformatics 07-20-2011, 09:27 AM
Replies: 3
Views: 2,765
Posted By malcook
Here is a strategy, assuming that each...

Here is a strategy, assuming that

each sam file has at most one alignment per read
the sam files are not (yet) sorted

Use `samtools view` to extract just the alignments from each file
...
Forum: Bioinformatics 06-10-2011, 10:30 PM
Replies: 10
Views: 3,529
Posted By malcook
fastx toolkit

http://hannonlab.cshl.edu/fastx_toolkit/
Forum: Bioinformatics 06-09-2011, 08:28 AM
Replies: 3
Views: 1,892
Posted By malcook
tabulating gaps in bam files using bioconductor's GenomicRanges IS POSSIBLE

I think you may misunderstand the manual. In any case, the key word in your comment is perhaps "directly" ;)

I've just blogged on using GenomicRanges for this exact purpose here...
Forum: Bioinformatics 11-02-2010, 11:24 AM
Replies: 3
Views: 3,354
Posted By malcook
http://code.google.com/p/bedtools/

http://code.google.com/p/bedtools/
Forum: Illumina/Solexa 10-08-2010, 08:31 AM
Replies: 4
Views: 4,412
Posted By malcook
galaxy ++

And, plans like these (http://lists.bx.psu.edu/pipermail/galaxy-user/2010-October/001493.html) make it sound even more attractive...
Forum: Bioinformatics 09-08-2010, 06:49 AM
Replies: 10
Views: 4,155
Posted By malcook
consolidating pileup across multiple samples

Here are steps for using samtools to creating pileup output for three samples holding the sample allele at each site

# assuming for each of three read groups (samples) named s1,s2,s3 that you have...
Forum: Bioinformatics 08-20-2010, 07:44 AM
Replies: 513
Views: 200,001
Posted By malcook
Warning: Exhausted best-first chunk memory for read

when I get this message I have found that the following option makes it go away (doubling the default value)

--chunkmbs 128
Forum: Bioinformatics 06-01-2010, 06:10 PM
Replies: 1
Views: 1,896
Posted By malcook
looks like varscan will do this itself using the...

looks like varscan will do this itself using the compare subcommand which is documented (http://sourceforge.net/apps/mediawiki/varscan/index.php?title=Main_Page) to "Merge/intersect/substract 2 sets...
Forum: Bioinformatics 04-27-2010, 07:24 PM
Replies: 7
Views: 2,060
Posted By malcook
bam bam bam bam

BAM format (http://samtools.sourceforge.net/) is supported by IGV (http://www.broadinstitute.org/igv/AlignmentData) as well as by UCSC (http://genome.ucsc.edu/goldenPath/help/bam.html) and is just...
Forum: Bioinformatics 04-26-2010, 07:00 PM
Replies: 4
Views: 1,750
Posted By malcook
IGV (http://www.broad.mit.edu/igv/) displays the...

IGV (http://www.broad.mit.edu/igv/) displays the spliced alignments produced by Tophat just fine.
Forum: Academic/Non-Profit Jobs 02-08-2010, 09:15 AM
Replies: 0
Views: 1,505
Posted By malcook
Stowers Institute for Medical Research (Kansas City) positions

The Stowers Institute for Medical Research has two openings for Programmer Analysts to:

* provide operational and data analysis support for Next-Generation DNA Sequencing Informatics processes. ...
Forum: Bioinformatics 02-04-2010, 06:36 AM
Replies: 43
Views: 20,324
Posted By malcook
Igv

IGV architect/developer Jim Robinson told me that he might implement a URL API for navigating the browser, in addition to existing method of listening for navigation commands on a port...
Forum: Bioinformatics 01-26-2010, 06:27 AM
Replies: 0
Views: 1,328
Posted By malcook
should I mask the pseudoautosomal segments of human genome?

What do you think of my plan to mask the pseudoautosomal segments of human Y chromosome prior to running bowtie on an RNASeq project?

Since pseudoautosomal portion of human genome chromosomes X &...
Forum: Bioinformatics 01-22-2010, 09:35 AM
Replies: 513
Views: 200,001
Posted By malcook
bowtie: should I mask the pseudoautosomal segments of human genome

What do you think of my plan to mask the pseudoautosomal segments of human Y chromosome prior to running bowtie on an RNASeq project.

Since pseudoautosomal portion of human genome chromosomes X &...
Forum: Bioinformatics 12-23-2009, 08:43 AM
Replies: 6
Views: 4,989
Posted By malcook
hmmm - I don't see any mappability in either...

hmmm - I don't see any mappability in either human or mouse at ucsc. (sounds of poking around) Oh, I see, it exists for human in hg18 but not most recent hg19. OK. Interesting. Thanks!

The...
Forum: Bioinformatics 12-22-2009, 02:18 PM
Replies: 6
Views: 4,989
Posted By malcook
method for computing "mappable" regions of genome

The program vmatch [1] can be used to find all pairs of regions longer than a length that are similar (or identical) to each other, where similarity can be defined in terms of maximum edit or hamming...
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