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Search: Posts Made By: rama
Forum: Bioinformatics 04-04-2014, 03:49 PM
Replies: 3
Views: 967
Posted By rama
Hi Tom, have you tried gitools...

Hi Tom,

have you tried gitools (http://www.gitools.org/home)?
Forum: Bioinformatics 09-24-2013, 10:16 AM
Replies: 9
Views: 4,658
Posted By rama
Hi yasashiku, Thanks a bunch for your kind...

Hi yasashiku,

Thanks a bunch for your kind reply. I am going to try your 1st suggestion as this seem to be the most common according to the GATK forums.

Rama
Forum: Bioinformatics 09-23-2013, 12:52 PM
Replies: 9
Views: 4,658
Posted By rama
hi yasashiku, I am dealing with the same...

hi yasashiku,

I am dealing with the same issue and came across your post hear while searching for help. so wondering if you ever found the way to address this problem. if so, could you please...
Forum: General 07-01-2013, 11:01 AM
Replies: 2
Views: 2,157
Posted By rama
hi, just wondering if you ever got through...

hi, just wondering if you ever got through figuring this out. I would really appreciate your thoughts on how we could address the same problem that we have right now.

thanks
Forum: Bioinformatics 06-24-2013, 03:45 PM
Replies: 7
Views: 2,203
Posted By rama
Thanks a bunch for the pointer. once we...

Thanks a bunch for the pointer.
once we identify the data with "high quality set" is there a way to compute metrics at different coverage thresholds. I am not sure how to do it, do I have to...
Forum: Bioinformatics 06-24-2013, 02:11 PM
Replies: 7
Views: 2,203
Posted By rama
finding the depth of coverage with more confidence

This is an extension to the original question on this post. I was wondering if anybody knows how I can calculate the accuracy in sequencing at various levels of depth of coverage. based on this I...
Forum: Bioinformatics 01-15-2013, 08:21 AM
Replies: 7
Views: 2,001
Posted By rama
Thank you vivek.

Thank you vivek.
Forum: Bioinformatics 01-14-2013, 03:04 PM
Replies: 7
Views: 2,001
Posted By rama
Thank you Vivek, it worked like a charm. ...

Thank you Vivek, it worked like a charm.

just one more request, how do I group by chromosome to see the number of bases per chromosome covered by the target regions.
Forum: Bioinformatics 01-14-2013, 02:48 PM
Replies: 7
Views: 2,001
Posted By rama
Hi Vivek, Thanks for your reply. I am...

Hi Vivek,

Thanks for your reply.

I am not familiar with awk, I tried your commands but both gave 0 as result.
here I have copied first few lines from my bed file.
...
Forum: Bioinformatics 01-14-2013, 01:30 PM
Replies: 7
Views: 2,001
Posted By rama
calculate total number of unique positions in target regions

Hi there,

I have a bed file containing target regions and I want to calculate the total number of bases covered by these regions(total length of target regions) and also the number of unique base...
Forum: General 01-07-2013, 08:35 AM
Replies: 5
Views: 2,441
Posted By rama
does anyone have an explanation why the number...

does anyone have an explanation why the number variants vary significantly between release/20100804 and 20110521 for any sample. I looked for the variants listed for NA10851 sample from...
Forum: Bioinformatics 12-13-2012, 08:42 AM
Replies: 36
Views: 63,452
Posted By rama
Thanks Laura, for trying it out.

Thanks Laura, for trying it out.
Forum: Bioinformatics 12-12-2012, 03:58 PM
Replies: 36
Views: 63,452
Posted By rama
Hi Laura, I am still having trouble with...

Hi Laura,

I am still having trouble with extracting the variant calls of a specific sample.

As you pointed out earlier that I have downloaded sites file with no genotype column, so now I got...
Forum: Bioinformatics 12-07-2012, 12:36 PM
Replies: 36
Views: 63,452
Posted By rama
Laura, I tried with downloading both the...

Laura,

I tried with downloading both the vcf.gz and tbi files. but it did not work and it is difficult to interpret the error. can you see what I am doing wrong here

./tabix -h...
Forum: Bioinformatics 12-06-2012, 05:37 PM
Replies: 36
Views: 63,452
Posted By rama
Laura, how/what should I specify, if I don't...

Laura,

how/what should I specify, if I don't have particular region to look at and want to get all genome-wide variants?

Thanks so much for you kind help.
Forum: Bioinformatics 12-06-2012, 10:35 AM
Replies: 36
Views: 63,452
Posted By rama
Laura, Thanks much for your reply. I am...

Laura,

Thanks much for your reply. I am guessing this is the example for getting the vcf of sample.

tabix -h ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4in......
Forum: Bioinformatics 12-05-2012, 03:18 PM
Replies: 36
Views: 63,452
Posted By rama
vcf file of specific sample from 1000Genome data

Hi,

Can anyone help me how to access the vcf file of a specific sample from 1000Genome data. I found the consensus file at (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release) but couldn't find...
Forum: Bioinformatics 11-07-2012, 02:12 PM
Replies: 2
Views: 1,433
Posted By rama
Thank you, I never used it but sure will give a...

Thank you, I never used it but sure will give a try.
Forum: Bioinformatics 11-07-2012, 01:40 PM
Replies: 2
Views: 1,433
Posted By rama
exon and intron numbers of genes

Hi All,

Please excuse me if this is going to be a repeat of any earlier post, I have been searching through various posts thinking someone must have asked this before but couldn't find.
I have a...
Forum: Bioinformatics 09-04-2012, 10:38 AM
Replies: 8
Views: 7,428
Posted By rama
Hi,

I was wondering if you ever got this problem solved. I am now having the same problem and when I searched online found your post. I will be grateful if you can share with me how you resolved this...
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