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Forum: Bioinformatics 03-18-2012, 11:05 AM
Replies: 1
Views: 2,957
Posted By polsum
edgeR Normalization question

The edgeR manual gives us three examples for DE analysis with each example normalizing the data in different manner.

In the case study 1, the Normalization was done by calcNormFactors. In the case...
Forum: Bioinformatics 03-06-2012, 09:47 AM
Replies: 0
Views: 646
Posted By polsum
Multiple Alignment of miRNAs with Precursors

Hi I am looking for a program that can align all miRNA variants or isomirs to the precursers and produce a map like below. Can you please suggest a program for that? thanks in advance.
...
Forum: Bioinformatics 02-04-2012, 11:47 AM
Replies: 5
Views: 3,265
Posted By polsum
Simon, this precisely is my question. The...

Simon, this precisely is my question. The function 'getVarianceStabilizedData' uses 'cds' as the argument which doesnt have same structure as argument 'd' generated by EdgeR. My question is how to...
Forum: Bioinformatics 02-03-2012, 04:14 PM
Replies: 5
Views: 3,265
Posted By polsum
EdgeR: Heatmaps

Hi, I know DESeq can make some really nice heat maps along with clustering of the differentially expressed genes. How can I make such maps with edger? Can I import edgeR data to Deseq to make those...
Forum: Bioinformatics 01-20-2012, 12:57 PM
Replies: 23
Views: 47,764
Posted By polsum
No I meant "if ((FDR < 0.085) AND (p.value <...

No I meant "if ((FDR < 0.085) AND (p.value < 0.05))...no "fishing" or "fishy" business here. I am genuinely curious, how would any one sets the cutoff? There is no consensus in published literature...
Forum: Bioinformatics 01-20-2012, 12:01 PM
Replies: 23
Views: 47,764
Posted By polsum
edgeR: How important is the FDR value?

Hi,

I was wondering if any one can answer my question about FDR

How exactly we should determine the cutoff limit for FDR value? Is 0.1 acceptable or 0.2? Because the number of significantly...
Forum: Bioinformatics 12-23-2011, 08:57 PM
Replies: 3
Views: 1,841
Posted By polsum
How do you account for multiple mappings? if a...

How do you account for multiple mappings? if a read maps on more than 1 genomic location, how do you assign the read to different mappings? thanks.
Forum: Bioinformatics 12-14-2011, 10:45 AM
Replies: 2
Views: 4,207
Posted By polsum
I have the same question. I will wait for the...

I have the same question. I will wait for the experts to answer.
Forum: Bioinformatics 12-02-2011, 12:17 PM
Replies: 2
Views: 1,791
Posted By polsum
Ok I was using 32-bit OS and I removed it and...

Ok I was using 32-bit OS and I removed it and installed 64-Bit OS and its working without any problems. Apparently 32-bit version cant use more than 4GB memory.
Forum: Bioinformatics 12-01-2011, 02:29 PM
Replies: 2
Views: 1,791
Posted By polsum
Bowtie memory error

Hi - I am getting following error with bowtie

"Error: Could not allocate ChunkPool of 67108864 bytes
terminate called after throwing an instance of 'int'"

Our computer has 12 GB memory with...
Forum: Bioinformatics 11-30-2011, 03:54 PM
Replies: 2
Views: 1,728
Posted By polsum
cw1 thanks. I copied the header lines of one...

cw1

thanks. I copied the header lines of one file and pasted in the second file and then had no problems.
Forum: Bioinformatics 11-30-2011, 12:16 PM
Replies: 2
Views: 1,728
Posted By polsum
cufflinks error

Hi I am comparing two Bam files with cuffdiff but I get the following error.

Error: sort order of reads in BAMs must be the same

I use bowtie to produce sam files, convert them to bam and sort...
Forum: Bioinformatics 11-28-2011, 11:15 PM
Replies: 19
Views: 10,626
Posted By polsum
a dumb question. How did you make that figure in...

a dumb question. How did you make that figure in the first post of this thread? which program you used?
Forum: Bioinformatics 11-22-2011, 09:35 AM
Replies: 8
Views: 8,029
Posted By polsum
Thank you very much. This script cleaned my file...

Thank you very much. This script cleaned my file and now its running just fine.
Forum: Bioinformatics 11-21-2011, 10:20 AM
Replies: 8
Views: 8,029
Posted By polsum
Unhappy FastQC Problem

Hi while using FastQC, I am getting following error.

uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
at...
Forum: Bioinformatics 11-08-2011, 09:10 AM
Replies: 4
Views: 1,026
Posted By polsum
Thank you very much cjp, this is exactly what I...

Thank you very much cjp, this is exactly what I am looking for. :)
Forum: Bioinformatics 11-08-2011, 08:40 AM
Replies: 4
Views: 1,026
Posted By polsum
No one? :confused: I am pretty sure some of you...

No one? :confused: I am pretty sure some of you might have encountered same question or problem. Thanks in advance.
Forum: Bioinformatics 11-07-2011, 10:24 AM
Replies: 4
Views: 1,026
Posted By polsum
Question Multiple Mappings

Hi - I have shortRNA NGS data and there are many short reads that map to multiple types of microRNAs and some microRNAs and genes. To which type of microRNA or gene should I assign this read?

For...
Forum: Bioinformatics 08-04-2011, 10:38 AM
Replies: 1
Views: 2,948
Posted By polsum
Differential Expression analysis without replicates

Hi, I would like to know the best statistical method or program to perform differential expression analysis of solexa/illumina based deep sequenced reads between two samples.

Does anyone has an...
Forum: Bioinformatics 06-19-2010, 03:59 PM
Replies: 11
Views: 8,473
Posted By polsum
Ok I just found out. Save the bowtie output in...

Ok I just found out. Save the bowtie output in Sam format, convert it to Bam format by samtools and convert Bam to BED by Bedtools.
Forum: Bioinformatics 06-18-2010, 04:31 PM
Replies: 11
Views: 8,473
Posted By polsum
Bowtie output to BED format

Hi - Can any one please suggest a method to convert Bowtie output to BED format? Is there a bioperl script or any software for that?

thanks in advance.
Forum: Bioinformatics 06-12-2010, 10:37 AM
Replies: 1
Views: 1,151
Posted By polsum
Bowtie nor mapping to RNA database

Does bowtie recognize only T and not U? When I used RNA database none of my reads mapped to it, but when changed U to T then they mapped. am I missing something? thanks.
Forum: Bioinformatics 06-02-2010, 02:00 PM
Replies: 2
Views: 1,865
Posted By polsum
Bowtie Build 64-bit

Hi - Bowtie itself is very fast, but bowtie-build takes lots of time to build the indexes. Where do I download the 64-bit version of bowtie-build? I cant locate it in the bowtie wesite.

thanks in...
Forum: Bioinformatics 05-18-2010, 09:38 AM
Replies: 1
Views: 2,264
Posted By polsum
Bowtie database index question

Hi

I am trying to map illumina deepsequenced shortRNA transcripts to different types of RNA databases such as miRNA, piRNA, rRNA etc.

Is it a good idea to map the reads separately to each...
Forum: Bioinformatics 07-31-2009, 08:33 AM
Replies: 65
Views: 31,017
Posted By polsum
Hi, I have been testing the trial version of CLC...

Hi, I have been testing the trial version of CLC workbench and I encountered two issues.

1. I BLASTed a set of illumina generated short reads (17-33, after trimming the 3'adapters) to mouse RefSeq...
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