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Forum: Bioinformatics 07-03-2014, 08:02 PM
Replies: 0
Views: 935
Posted By a_mt
mutSig on target capture data

Hi all,

As the title goes, can we use MutSig on the data obtained from targetted capture sequencing of around 500 genes to detect significantly affected genes ?

My guess is because of...
Forum: Bioinformatics 06-26-2014, 07:04 PM
Replies: 1
Views: 1,678
Posted By a_mt
some basic questions about duplicate removal ?

Hi all,

I am using the GATK pipeline for pre processing bam files after alignment with bwa mem. The original bam files after alignment shows I have (samtools flagstat command) - 173,460,757 reads...
Forum: Bioinformatics 04-29-2014, 10:46 PM
Replies: 2
Views: 4,632
Posted By a_mt
Hi, Thank you very much for the reply....

Hi,

Thank you very much for the reply. XT:A:U tag works fine :)
Forum: Bioinformatics 04-28-2014, 10:25 PM
Replies: 2
Views: 4,632
Posted By a_mt
Question Uniquely mapped reads from BAM file (BWA)

Hi all,

I know this question has been asked many times. But, I am still not able to find the proper answer. So, how do you caluclate the number of uniquely mapped reads from BAM file generated by...
Forum: Bioinformatics 10-31-2013, 04:54 AM
Replies: 22
Views: 19,357
Posted By a_mt
Hi feralBiologist, There's a qucik way to do...

Hi feralBiologist,

There's a qucik way to do it:

1. convert your SAM/BAM to wiggle file (you can use bedtools)

2. multiply every value in wiggle by (1,000,000/no. of reads)

for eg: if...
Forum: Bioinformatics 10-30-2013, 12:47 AM
Replies: 2
Views: 1,231
Posted By a_mt
are these motifs same ?

Hi all,

I was doing motif analysis in two phenotypes of the same species and found two motifs. In phenotype-A, poly-A regions was over-represented whereas in phenotype-B, ploy-T region was...
Forum: Bioinformatics 09-25-2013, 03:15 AM
Replies: 4
Views: 1,447
Posted By a_mt
Hi Adrian, There's a qucik way to do it: ...

Hi Adrian,

There's a qucik way to do it:

1. convert your SAM/BAM to wiggle file (you can use bedtools or check this (http://seqanswers.com/forums/showthread.php?t=7379))

2. multiply every...
Forum: Bioinformatics 09-23-2013, 03:04 AM
Replies: 1
Views: 1,587
Posted By a_mt
in simple terms: coverage=(no. of reads *...

in simple terms: coverage=(no. of reads * read_length)/genome_size
Forum: Bioinformatics 09-17-2013, 08:22 PM
Replies: 4
Views: 2,036
Posted By a_mt
why dont you install it from repository:

why dont you install it from repository:
Forum: Bioinformatics 09-17-2013, 03:08 AM
Replies: 5
Views: 2,135
Posted By a_mt
Hi, There is this paper...

Hi,

There is this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877578/) where they have measured effect of cis and trans regulatory elements on gene expression between two closely related...
Forum: Bioinformatics 09-10-2013, 08:50 PM
Replies: 2
Views: 1,712
Posted By a_mt
In bowtie2 if a read aligns to multiple locations...

In bowtie2 if a read aligns to multiple locations it has XS tag. You can simply use sed to delete lines with this tag, if this is what you wanted.
Forum: Bioinformatics 07-12-2013, 09:35 PM
Replies: 6
Views: 2,232
Posted By a_mt
Yes.. I am demultiplexing them separately.. ...

Yes.. I am demultiplexing them separately..

If you don't mind, can you suggest me any such tools you might be familiar with, performance wise... There are lot of such tools (1...
Forum: Bioinformatics 07-12-2013, 09:11 PM
Replies: 6
Views: 2,232
Posted By a_mt
I don not have much information on edit distance....

I don not have much information on edit distance. But it seems to be around 6-7, and barcodes are 19mers (sorry a typo at the beginning, it isn't 13).

I want to align them as single end,...
Forum: Bioinformatics 07-12-2013, 12:58 AM
Replies: 6
Views: 2,232
Posted By a_mt
My barcodes are 13mers and yes it is multiplexing...

My barcodes are 13mers and yes it is multiplexing of 96 samples. Guess I will use strict mapping.

I have another question though. After demultiplexing I got some samples with very few common...
Forum: Bioinformatics 07-11-2013, 08:16 PM
Replies: 6
Views: 2,232
Posted By a_mt
Question effective mismatches allowed while demultiplexing

Hi all,

What is the minimum/optimum number of mismatches to be allowed during demultiplexing ?? How do we decide this?

I am demultiplexing using fastx-barcode splitter, allowing 4 mismatches...
Forum: Bioinformatics 04-28-2013, 11:06 PM
Replies: 5
Views: 2,190
Posted By a_mt
ok.. not arguing.. but for your reference ...

ok.. not arguing.. but for your reference

http://www.biomedcentral.com/1471-2105/14/91#B7

and a quote from DESeq paper :



quote from DEGseq...
Forum: Bioinformatics 04-28-2013, 10:51 PM
Replies: 5
Views: 2,190
Posted By a_mt
Sorry, I meant to say in general count data...

Sorry, I meant to say in general count data follows poisson distribution.
But,is it ok to use vsd normalized data to detect DE genes ?? and I don't have any replicates..
Forum: Bioinformatics 04-28-2013, 09:57 PM
Replies: 5
Views: 2,190
Posted By a_mt
Question finding DE genes from VSD normalized data

Hi all,

I have time series mRNA-seq data but without replicates.
I have some doubts about calling DE genes with DESeq.

I have used varianceStabilizingTransformation function from DESeq to...
Forum: Bioinformatics 02-19-2013, 09:14 PM
Replies: 0
Views: 1,165
Posted By a_mt
Post splitting longer reads into two smaller reads for bowtie input

Hi all,

I have sequence data from Illumina GA with read length of 95 bp's (after trimming).
Now I am using a tool which works with bowtie. Since my read length is above 50bp's and bowtie doesn't...
Forum: Bioinformatics 01-18-2013, 11:43 PM
Replies: 4
Views: 2,126
Posted By a_mt
@GenoMax : You were right.. I used...

@GenoMax :

You were right.. I used different number of cores this is what I found (attachment). At -p 30, it took about only 1 min 30 seconds, after that it went on increasing. I think this is...
Forum: Bioinformatics 01-17-2013, 09:09 PM
Replies: 55
Views: 33,256
Posted By a_mt
Hi bmtb, I hope this is what you are looking...

Hi bmtb,

I hope this is what you are looking for. Even I had the same problem where reads in forward and reverse files were not in order. I use this shell script to extract common reads and orphan...
Forum: Bioinformatics 01-17-2013, 08:51 PM
Replies: 4
Views: 2,126
Posted By a_mt
Post alignment speed on workstation vs desktop

Hi all,

Recently our lab purchased a workstation with 64 GB RAM, xeon processor (which has 64 cores) running on 64bit linux. I am connected to it through a desktop (linux 64bit) which has 4GB RAM,...
Forum: Bioinformatics 12-23-2012, 09:15 PM
Replies: 6
Views: 3,360
Posted By a_mt
how about NGS QC Toolkit...

how about NGS QC Toolkit (http://59.163.192.90:8080/ngsqctoolkit/).


Implemented in perl.
Forum: Bioinformatics 12-22-2012, 12:32 AM
Replies: 5
Views: 2,350
Posted By a_mt
Yes, sequence files were given to me by our...

Yes, sequence files were given to me by our sequence provider, which I demultiplexed. But after demultiplexing this is the result. May be there is an issue with this. Anyways I will contact them....
Forum: Bioinformatics 12-21-2012, 11:57 PM
Replies: 5
Views: 2,350
Posted By a_mt
Thanks for the snippet jiaco. Even I had tried...

Thanks for the snippet jiaco.
Even I had tried this before but this aslso messes up with quality score line which are ending with +

And also there are reads having empty lines in between. My...
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