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Forum: RNA Sequencing 04-09-2012, 12:31 PM
Replies: 1
Views: 2,721
Posted By swapnil2188
Can VarScan be used to find out Somatic Mutations in RNA seq Data ?

Hello,
I am trying to find out Somatic mutations Using VarScan in RNA seq Data.
Can Varscan detect them in RNA seq ?

1. Has anyone used it previously on RNA ?

2. I used the following steps:
...
Forum: RNA Sequencing 04-09-2012, 12:14 PM
Replies: 2
Views: 2,342
Posted By swapnil2188
Please can Anyone help me with this ? I am...

Please can Anyone help me with this ?

I am waiting for response !

Thank You !
Forum: RNA Sequencing 04-05-2012, 10:08 AM
Replies: 2
Views: 2,342
Posted By swapnil2188
Doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)


The two .bam files or samples I am comparing include multiple samples merged together into them (3...
Forum: General 03-26-2012, 12:26 PM
Replies: 1
Views: 1,311
Posted By swapnil2188
Problems with finding out indels using Unified Genotyper ? using GATK

Problems with finding out indels using Unified Genotyper ? (GATK)

I followed the std protocol of First base reaclibarting the .bam file followed by using the realigned .bam file to call for SNPs...
Forum: General 03-26-2012, 12:19 PM
Replies: 2
Views: 3,702
Posted By swapnil2188
Samtools mpileup - Call somatic mutations from a pair of samples - detail steps ?

Can any one please clear some doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf
...
Forum: RNA Sequencing 02-24-2012, 10:00 AM
Replies: 3
Views: 1,714
Posted By swapnil2188
As you said, you worked on known variants- I...

As you said, you worked on known variants- I would like to know that whether you worked on Human samples ? Also, you said you did same with Arabidopsis (RNA seq data) for which you had to prepare...
Forum: RNA Sequencing 02-21-2012, 08:19 AM
Replies: 3
Views: 1,714
Posted By swapnil2188
Annotating RNA seq Data ?

I am trying to find out variants in RNA seq data.

I have the .bam files for the samples.

I will try and use Samtools and GATK to find out variants in RNA.

Now, as I am using Samtools I will...
Forum: Ion Torrent 02-16-2012, 01:30 PM
Replies: 5
Views: 3,838
Posted By swapnil2188
TMAP installation Problem

I tried running this command

sh autogen.sh && ./configure && make

I got error............. saying

make[2]: *** [src/index/tmap_bwt_aux.o] Error 1

make[2]: Leaving directory...
Forum: RNA Sequencing 02-11-2012, 04:52 PM
Replies: 2
Views: 7,506
Posted By swapnil2188
Any one please help me with this. How should...

Any one please help me with this.

How should I calculate RPM values for a gene list ?
Forum: RNA Sequencing 02-07-2012, 10:21 AM
Replies: 2
Views: 7,506
Posted By swapnil2188
How to Calculate RPM value for gene

How can I calculate RPM value for a gene to validate my results ?
Forum: RNA Sequencing 02-06-2012, 12:03 PM
Replies: 4
Views: 2,539
Posted By swapnil2188
Thanks.............!!!!!!!!!! I guess this might...

Thanks.............!!!!!!!!!! I guess this might help
I will try both GATK and samtools.

Here a found a list to analyse seq data..........

http://seqanswers.com/wiki/Software/list

I thought...
Forum: RNA Sequencing 02-02-2012, 01:17 PM
Replies: 4
Views: 2,539
Posted By swapnil2188
Tools or ways to find out variants in RNA seq data ?????

I know that we can find out variants in DNA seq data using different tools(GATK, Samtools..........) but I wonder if there are any tools to find out variants in RNA seq data.

I understand the...
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