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Forum: Literature Watch 04-05-2012, 05:09 AM
Replies: 46
Views: 44,009
Posted By pd
Can't use an undefined value as an ARRAY reference

While running CNV-seq, sometimes it works perfectly but sometimes i end with the following error "Can't use an undefined value as an ARRAY reference at line 205, <REF> line 1119928258".
...
Forum: Bioinformatics 01-24-2012, 03:00 AM
Replies: 4
Views: 2,933
Posted By pd
thank you ganygan25

thank you ganygan25
Forum: Bioinformatics 01-23-2012, 06:42 AM
Replies: 4
Views: 2,933
Posted By pd
readme fiel not clear

Hi

The cnvNMM READMe file is not clear. I could not figure out the format or type of cnsfile. Some idea?
Forum: Bioinformatics 11-27-2011, 08:37 AM
Replies: 22
Views: 7,299
Posted By pd
bwa sampe gives different output..

Hi all

I am trying to use sampe program from bwa with 3 options -P -s -a.. Here only -a option requires integer values to be provided. So how to specify these option in the command line because i...
Forum: Literature Watch 11-24-2011, 02:46 AM
Replies: 46
Views: 44,009
Posted By pd
Thank you dinesh. But my data is not...

Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??
Forum: Literature Watch 11-24-2011, 02:34 AM
Replies: 46
Views: 44,009
Posted By pd
CNV-seq ref.hits file?

Hello

I am analyzing CNVs for the first time or rather new to CNV-seq. Manual is pretty clear but i have one very basic doubt. I have my .bam file for which i can generate my.hits file as well...
Forum: Bioinformatics 11-24-2011, 01:12 AM
Replies: 9
Views: 13,529
Posted By pd
picard CleaneSam.jar option

Hello

I have some CIGAR length problem in one of my sequence in .sam file. Anyone had any idea about the picard CleanSam.jar option from picard tools.. What actually it does?? Or it would be good...
Forum: Bioinformatics 11-17-2011, 05:39 AM
Replies: 10
Views: 4,192
Posted By pd
thank you... cheers.

thank you... cheers.
Forum: Bioinformatics 11-17-2011, 05:39 AM
Replies: 9
Views: 13,529
Posted By pd
yes the file was unsorted. Once i sorted it,...

yes the file was unsorted. Once i sorted it, worked excellently. But facing one more problem now. :-).. WHICH IS
SAM validation error: ERROR: Record 7181005, Read name...
Forum: Bioinformatics 11-17-2011, 04:28 AM
Replies: 17
Views: 28,566
Posted By pd
conert only a part of sam file to bam?

HI

Is there any option by which i can convert only apart of sam file to bam because sam file is having some problem with CIGAR length.
Forum: Bioinformatics 11-17-2011, 12:52 AM
Replies: 6
Views: 6,012
Posted By pd
CIGAR and Sequence length are inconsistent

Dear,

I am trying to convert sam file to bam file. I am pretty new to this conversion. But i got the following error :CIGAR and SEQUENCE length are inconsistent.
Is there a quick tool for...
Forum: Bioinformatics 11-15-2011, 03:22 AM
Replies: 10
Views: 4,192
Posted By pd
TRimming FASTQ file

Dear,

I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do...
Forum: Bioinformatics 11-14-2011, 03:44 AM
Replies: 9
Views: 13,529
Posted By pd
Exclamation Picard error in CollectMultipleMetrics.jar

Hi

I am trying to use picard tool - CollectMultipleMetrics.jar to find out the insert size distribution. Unfortunately when i run the following command
"java -jar CollectMultipleMetrics.jar...
Forum: Bioinformatics 08-31-2011, 11:08 PM
Replies: 57
Views: 43,408
Posted By pd
perl scripts for conversion of bowtie output to .gff and .wig files

Originally Posted by graveley View Post
Dear Yogesh,

We do this by writing a perl script that reads in the alignment information and writes a new file in the appropriate format. I would send you...
Forum: Bioinformatics 07-29-2011, 04:50 AM
Replies: 66
Views: 30,872
Posted By pd
Too many peaks generated using Cisgenome V2 (seqpeak)

Hi friends
I have a strange query. I ran cisgenome for single Lane alone and in replicates as well with Input DNA as control. The problem which i'm is regarding the number of peaks. When i use the...
Forum: Bioinformatics 05-24-2011, 02:52 AM
Replies: 66
Views: 30,872
Posted By pd
Hello Hji

I had already cross checked both the things which you have mentioned that is a) Using the same build e.g. hg18 in both Cisgenome and UCSC and b) considering the offset of 1. But i still get the...
Forum: Bioinformatics 05-22-2011, 10:26 PM
Replies: 66
Views: 30,872
Posted By pd
Hello Hji I had a small query regarding...

Hello Hji
I had a small query regarding retrieval of peak's sequences from cisgenome and UCSC. When i use the Get Sequence option in CisGenome, the fetched sequence from cisgenome never matches to...
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