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Search: Posts Made By: JohnK
Forum: General 12-22-2011, 08:44 AM
Replies: 9
Views: 1,621
Posted By JohnK
Perl is nice, and it is what I started with years...

Perl is nice, and it is what I started with years ago. Believe it or not, the book that did it all for me was "Beginning Perl for Bioinformatics". From this book I gathered a strong foundation in...
Forum: Bioinformatics 06-06-2011, 11:09 AM
Replies: 8
Views: 2,137
Posted By JohnK
Essentially, you're removing them because you...

Essentially, you're removing them because you can't disambiguate whether the read came from a unique bead source versus PCR. IMO, I removed PCR dups based on start and stop alone, because PCR has an...
Forum: Bioinformatics 03-25-2011, 01:22 PM
Replies: 2
Views: 1,530
Posted By JohnK
dbSNP frequencies

I recently had someone ask for some dbSNP frequencies. Does anyone know what file to use to get MAF frequencies for SNPs with rsIDs listed by ID and, or allele? I've downloaded some files and...
Forum: Bioinformatics 03-09-2011, 10:04 AM
Replies: 16
Views: 14,265
Posted By JohnK
It's not too high necessarily. It really depends...

It's not too high necessarily. It really depends on starting DNA quantity and how much you PCR it up. I've seen between 30% and even up to over 80% depending on the context of the protein we're...
Forum: RNA Sequencing 03-07-2011, 10:32 AM
Replies: 23
Views: 7,684
Posted By JohnK
Hey, Vanessa. Not so much the fragmentation of...

Hey, Vanessa. Not so much the fragmentation of the RNA, but the poly(A) purification step, which you might expect to definitely generate a 3' bias as someone stated above... What do you think of...
Forum: RNA Sequencing 03-05-2011, 01:34 PM
Replies: 23
Views: 7,684
Posted By JohnK
Hi, Vanessa. So, would you say it's definitely a...

Hi, Vanessa. So, would you say it's definitely a result of the poly(A) selection?? Thanks!
Forum: RNA Sequencing 03-03-2011, 10:38 AM
Replies: 23
Views: 7,684
Posted By JohnK
Hi, irit. No doubt that polyA enrichment sounds...

Hi, irit. No doubt that polyA enrichment sounds like a perfect culprit. What are your thoughts on cDNA fragmentation though? From "RNA-Seq: a revolutionary tool for transcriptomics":
...
Forum: RNA Sequencing 03-03-2011, 09:39 AM
Replies: 23
Views: 7,684
Posted By JohnK
3' Bias in RNA-Seq

Would anyone happen to know what the specific factor in cDNA fragmentation is that causes the 3' bias? It seems I've read a few papers that mention the bias, but don't go into explaining why? Thank...
Forum: Bioinformatics 03-02-2011, 06:57 AM
Replies: 7
Views: 2,932
Posted By JohnK
Thank you, Harold!

Thank you, Harold!
Forum: Bioinformatics 03-01-2011, 01:38 PM
Replies: 7
Views: 2,932
Posted By JohnK
can you cite this? i tried to find it but had no...

can you cite this? i tried to find it but had no luck.
Forum: Bioinformatics 02-24-2011, 11:49 AM
Replies: 4
Views: 2,784
Posted By JohnK
in a file prog_name.pl: #!/usr/bin/perl ...

in a file prog_name.pl:

#!/usr/bin/perl

$in=$ARGV[0]; #input file name
$out=$ARGV[1];

open(FH, "< $in") || die "here1";
open(OUT, "> $out") || die "here2";
Forum: Bioinformatics 02-18-2011, 08:18 AM
Replies: 5
Views: 1,769
Posted By JohnK
I think your ideal insert size would be somewhere...

I think your ideal insert size would be somewhere along the lines of the maximum insert and read length that allows you to maximize the throughput of your sequencing platform without saturating your...
Forum: Bioinformatics 02-17-2011, 12:21 PM
Replies: 2
Views: 1,682
Posted By JohnK
Sweet! This sucks but thank you very much! ...

Sweet! This sucks but thank you very much! Going to work on it now...
Forum: Bioinformatics 02-17-2011, 09:28 AM
Replies: 2
Views: 1,682
Posted By JohnK
Variations off GATK

I have some Illumina data mapped via BowTie. Looking to call variations using the UnifiedGenotyper from GATK, but I keep getting this error:

Missing read group for read...
Forum: Bioinformatics 02-15-2011, 09:45 AM
Replies: 4
Views: 9,632
Posted By JohnK
Ah! thank you, epigen!!!

Ah! thank you, epigen!!!
Forum: Bioinformatics 02-15-2011, 08:13 AM
Replies: 4
Views: 9,632
Posted By JohnK
BCF Tools

Would anybody happen to know a link to where I can download BCF Tools?

J
Forum: Bioinformatics 02-14-2011, 07:49 AM
Replies: 1
Views: 521
Posted By JohnK
Optimal params for Bowtie

Hi, I'm hoping this isn't a re-post (maybe I didn't search the right keywords), but I'm looking for optimal parameters for some Illumina paired-end data I'd like to map via Bowtie. Does anyone have...
Forum: RNA Sequencing 02-09-2011, 01:05 PM
Replies: 15
Views: 3,915
Posted By JohnK
You might also want to check for fRNA...

You might also want to check for fRNA contamination. It's a possibility...
Forum: RNA Sequencing 02-09-2011, 09:11 AM
Replies: 15
Views: 3,915
Posted By JohnK
It could possibly be a number of things worth...

It could possibly be a number of things worth investigating including- PCR dup. removal (dependent on the number of PCR cycles you did), 5'/3' bias dependent on the method for creating your cDNA...
Forum: RNA Sequencing 02-09-2011, 08:35 AM
Replies: 15
Views: 3,915
Posted By JohnK
what gene model are you using?

what gene model are you using?
Forum: Bioinformatics 01-28-2011, 06:50 AM
Replies: 2
Views: 834
Posted By JohnK
its, thank you very much. i believe that's...

its, thank you very much. i believe that's exactly what i was looking for!
Forum: Bioinformatics 01-28-2011, 06:21 AM
Replies: 2
Views: 834
Posted By JohnK
Circle graphs

Does anybody know what those circular genome-maps are and if there is any software or modules that exist to create them? Thanks.

J
Forum: General 01-26-2011, 08:30 AM
Replies: 18
Views: 3,693
Posted By JohnK
i would convert thy wig files to .bw format and...

i would convert thy wig files to .bw format and get thee self a host of some sort so thee can upload thy bigWigs to thou's server and then thy may hurriedly view thy data set without having to endure...
Forum: Bioinformatics 01-14-2011, 03:06 PM
Replies: 27
Views: 3,114
Posted By JohnK
I talked to a colleague who sees these exon-peak...

I talked to a colleague who sees these exon-peak events in some of his data depending on what protein or transcription factor he's after. They could be perfectly valid.
Forum: Bioinformatics 01-13-2011, 09:43 AM
Replies: 27
Views: 3,114
Posted By JohnK
Possibility: Bias towards GC-rich content in...

Possibility:

Bias towards GC-rich content in fragment selection both in library prep and amplification before and during sequencing.

(Park, October 2009)
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