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Search: Posts Made By: Hena
Forum: Bioinformatics 08-19-2013, 12:20 AM
Replies: 2
Views: 2,198
Posted By Hena
I found an answer to why it does discard reads...

I found an answer to why it does discard reads even after minimum length.

https://github.com/jstjohn/SeqPrep/issues/3

Edit: If SeqPrep matches adapters but fails to do proper merge of reads,...
Forum: Bioinformatics 10-15-2012, 01:39 AM
Replies: 292
Views: 161,515
Posted By Hena
I did my own version of this in the end using...

I did my own version of this in the end using CIGAR string. However it does not take into account 'X', '=', 'N' or 'P' tags.

sub last_pos {
my @read = @_;
local $_;
my ($match,$del) =...
Forum: Bioinformatics 04-25-2012, 01:47 AM
Replies: 2
Views: 2,198
Posted By Hena
SeqPrep and discarding reads

I've been testing SeqPrep (http://seqanswers.com/wiki/SeqPrep) for trimming adapters and merging reads. However I'm unsure why some reads get discarded. The command line is as follows:

SeqPrep -f...
Forum: Bioinformatics 12-21-2011, 03:58 AM
Replies: 4
Views: 2,576
Posted By Hena
You can ask samtools mpileup to print out the...

You can ask samtools mpileup to print out the nucleotide pileups for each position in bam file. Parsing that should be fairly simple with a script.
Forum: Bioinformatics 12-21-2011, 03:53 AM
Replies: 0
Views: 1,650
Posted By Hena
dindel, exomes and chromosome 10

Hi all,

I run dindel as part of workflow which I do for dna seq, which large percent is exome samples. I've noticed something quite odd with regards to dindel stage 3.

I run stage 3 parallel...
Forum: Bioinformatics 08-05-2011, 02:04 AM
Replies: 292
Views: 161,515
Posted By Hena
Does anyone have nice perl snippet to calculate...

Does anyone have nice perl snippet to calculate the end point of the read in a sam file?
Forum: Bioinformatics 08-03-2011, 04:30 AM
Replies: 0
Views: 1,786
Posted By Hena
pileup file format

Hi all,

I'm trying to interpret the (m)?pileup file format with regarding to the indels. The documentation says that the indels have pattern [+-][0-9]+[ACGTNacgtn]+. After looking at the format it...
Forum: Bioinformatics 01-10-2011, 01:11 PM
Replies: 11
Views: 9,769
Posted By Hena
Is it the bwa sampe step which lasts long? I...

Is it the bwa sampe step which lasts long? I would suggest switching on the -P option (which loads the index into memory). That speeds up the execution quite a lot. It does require 4-5Gb of memory...
Forum: Bioinformatics 01-05-2011, 11:05 AM
Replies: 0
Views: 1,396
Posted By Hena
Coverage and deletions

Hi all,

I've been looking into using samtools mpileup to generate coverage. After converting its result to bedgraph format, I've compared it to a self generated one (directly from sam file) and...
Forum: Bioinformatics 10-25-2010, 10:51 PM
Replies: 30
Views: 10,797
Posted By Hena
Thanks for the answers lh3 and krobison. I got it...

Thanks for the answers lh3 and krobison. I got it running now :).
Forum: Bioinformatics 10-25-2010, 04:38 AM
Replies: 5
Views: 2,506
Posted By Hena
It depends on how the range is defined: 0 based...

It depends on how the range is defined: 0 based or 1 based positions? If one based, then 301 <= SNP_POSITION <= 500 is the range you had in the bed file.
Forum: Bioinformatics 10-25-2010, 04:28 AM
Replies: 30
Views: 10,797
Posted By Hena
Using dindel

Hi all,

I'm currently trying out dindel v0.12 (http://sites.google.com/site/keesalbers/soft/dindel) for finding indels. However I hit a little snag and there is little help available that I can...
Forum: Bioinformatics 05-03-2010, 01:23 AM
Replies: 24
Views: 34,426
Posted By Hena
What does that "never be an isolated Q2 basecall"...

What does that "never be an isolated Q2 basecall" really mean? I have this quality score

^``B`bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb`b`bcaaa`aab_a`caacca_]aaa`aaNY]]_]ab

Also how the region...
Forum: Bioinformatics 12-16-2009, 06:20 AM
Replies: 6
Views: 8,337
Posted By Hena
Yes, following lines. But the question is about...

Yes, following lines. But the question is about this line not following. Following line will have '*' in third column.
Forum: Bioinformatics 12-15-2009, 11:32 PM
Replies: 6
Views: 8,337
Posted By Hena
Why is there two ways of marking deletions? As...

Why is there two ways of marking deletions? As the page mentions that this '-[0-9]+[ACGTNacgtn]+' is a pattern for deletion. Also it seems that the * has a quality score in base quality column.

I...
Forum: Bioinformatics 12-15-2009, 04:40 AM
Replies: 6
Views: 8,337
Posted By Hena
Samtools - pileup format question

Hi,

I'm using pileup to make indel and snp calls. But I noticed a strangeness that isn't marked in the help page (http://samtools.sourceforge.net/pileup.shtml). There is a '*' in the read bases...
Forum: Bioinformatics 11-11-2009, 11:36 AM
Replies: 4
Views: 3,529
Posted By Hena
So then it essentially means in my example that...

So then it essentially means in my example that the second read of the pair is not mapped and it's values are not to be used for that read (though could be used for the 1st read).
Forum: Bioinformatics 11-10-2009, 02:58 AM
Replies: 4
Views: 3,529
Posted By Hena
Umm ... is there is guide that would tell me what...

Umm ... is there is guide that would tell me what that string representation means? As the result of that was:
HWI-EAS418:1:1:0:1819#0 pUr1 chr20 29366674 0 50M = ...
Forum: Bioinformatics 11-09-2009, 05:55 AM
Replies: 4
Views: 3,529
Posted By Hena
Understanding BWA result

Hi,

I've done some testing with BWA against couple of small chromosomes. My test data is paired end data. I don't understand couple lines of my results. I made a small perl script to understand...
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