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Search: Posts Made By: ersgupta
Forum: Bioinformatics 06-01-2015, 09:48 AM
Replies: 8
Views: 2,512
Posted By ersgupta
Hi Llopis, No problem. I was able to finally...

Hi Llopis,

No problem. I was able to finally resolve it, by making some array size adjustments to the code. thanks. :)
Forum: Bioinformatics 05-26-2015, 11:25 PM
Replies: 15
Views: 6,404
Posted By ersgupta
@sagarutturkar.. I will try that out. Thanks. :) ...

@sagarutturkar.. I will try that out. Thanks. :)

@r_sitaram... Thanks for the reply, I also found the same issue, had changed the array size in score.c, then it gave error in another file, then...
Forum: Bioinformatics 05-26-2015, 02:12 AM
Replies: 5
Views: 2,935
Posted By ersgupta
anybody has a solution for this error?

anybody has a solution for this error?
Forum: Bioinformatics 05-26-2015, 01:52 AM
Replies: 9
Views: 5,348
Posted By ersgupta
were you able to resolve the "score exited funny"...

were you able to resolve the "score exited funny" error?
Forum: Bioinformatics 05-18-2015, 03:55 AM
Replies: 8
Views: 2,512
Posted By ersgupta
Hi, Were you able to resolve the "ERROR 69:...

Hi,

Were you able to resolve the "ERROR 69: segmentation fault"? I am facing the same problem.
Forum: Bioinformatics 05-18-2015, 03:22 AM
Replies: 15
Views: 6,404
Posted By ersgupta
Hi, Were you able to resolve the "ERROR 69:...

Hi,

Were you able to resolve the "ERROR 69: segmentation fault"? I am facing the same problem.
Forum: Bioinformatics 05-21-2013, 04:48 AM
Replies: 29
Views: 30,158
Posted By ersgupta
@slees... i had the same problem, and this solved...

@slees... i had the same problem, and this solved it...

sudo cp /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib

:)
Forum: Bioinformatics 02-15-2013, 10:37 AM
Replies: 14
Views: 2,917
Posted By ersgupta
I have been using it for the past 6-8 months. I...

I have been using it for the past 6-8 months. I feel very happy when I am able to run my jobs using parallel, because just saves a hell lot of time. Actually it helps in best utilization of the...
Forum: Bioinformatics 02-15-2013, 10:29 AM
Replies: 2
Views: 1,249
Posted By ersgupta
I think BEDtools should be able to do this... ...

I think BEDtools should be able to do this...
For instance, you can merge the SNPs/INDELs(using mergeBed), use multiInteresectBed for getting SNPs/INDELs common to all cases, then use subtractBed...
Forum: Bioinformatics 12-18-2012, 11:18 PM
Replies: 1
Views: 1,938
Posted By ersgupta
Error while running ContEst

I am trying to run ContEst(http://www.broadinstitute.org/cancer/cga/contest)

Below is the command and options I used:

java -Xmx1200m -jar ContEst.jar \
-T Contamination \
-I test.bam...
Forum: Bioinformatics 12-14-2012, 04:18 AM
Replies: 7
Views: 22,052
Posted By ersgupta
try out "intersectBed" in bedtools... ...

try out "intersectBed" in bedtools...


http://code.google.com/p/bedtools/wiki/Usage#intersectBed
Forum: Bioinformatics 07-29-2012, 10:15 PM
Replies: 7
Views: 1,844
Posted By ersgupta
yeah the bed files can vary... which will...

yeah the bed files can vary... which will ultimately effect the statistics, one more thing i want to ask is 2100 included in the 2700 you get in case 2 ??
Forum: Bioinformatics 07-22-2012, 08:25 AM
Replies: 1
Views: 2,954
Posted By ersgupta
download the code and the database from the sift...

download the code and the database from the sift website and follow the instructions in the readme... i guess its pretty straight forward.. lemme knw if u have any specific doubt in that...
Forum: Bioinformatics 07-09-2012, 03:22 AM
Replies: 2
Views: 4,477
Posted By ersgupta
refer to this page...

refer to this page http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics
Forum: Bioinformatics 07-08-2012, 09:29 PM
Replies: 6
Views: 2,576
Posted By ersgupta
it works fine for me... except u cant go till...

it works fine for me... except u cant go till chr25.. u have to specify XY...
can u post a snapshot of the IGV.. ?
Forum: Bioinformatics 05-02-2012, 04:48 AM
Replies: 63
Views: 36,724
Posted By ersgupta
any update on the mpileup ?? :)

any update on the mpileup ?? :)
Forum: Bioinformatics 01-18-2012, 01:51 AM
Replies: 10
Views: 11,320
Posted By ersgupta
hi guys... i had also encountered d same error......

hi guys... i had also encountered d same error... i tried looking around for solution... but it turned out dat the file was not fully downloaded... so i guess u guys should also chek that...
Forum: Bioinformatics 11-18-2011, 11:47 PM
Replies: 15
Views: 6,544
Posted By ersgupta
can anybody explain me dis... many...

can anybody explain me dis...

many SRA(accession) ids having same SRP(study) id this is ok... as justified by an answer above...
but many SRP(study) ids having same SRA(accession) id...?
Forum: Bioinformatics 11-18-2011, 03:55 AM
Replies: 15
Views: 6,544
Posted By ersgupta
@nickloman... ok... will have a look at it...

@nickloman...

ok... will have a look at it as well... :)
Forum: Bioinformatics 11-18-2011, 03:34 AM
Replies: 15
Views: 6,544
Posted By ersgupta
I guess I can conclude this: "NCBI-SRA...

I guess I can conclude this:

"NCBI-SRA doesn't have a single ID using which we can get everything related to it i.e. study, run, experiment, sample", the only way to go about it is use the...
Forum: Bioinformatics 11-18-2011, 01:06 AM
Replies: 15
Views: 6,544
Posted By ersgupta
yeah... got it... That *.tab file is very useful...

yeah... got it... That *.tab file is very useful indeed... thanx... :)
Forum: Bioinformatics 11-17-2011, 03:55 AM
Replies: 15
Views: 6,544
Posted By ersgupta
This is a reply I got from a person in SRA. ...

This is a reply I got from a person in SRA.

The SRA number acts as a collector for the information. This means that when a center submits metadata or data they create a submission (SRAXXXXXX), but...
Forum: Bioinformatics 11-17-2011, 03:36 AM
Replies: 15
Views: 6,544
Posted By ersgupta
Both link to same page. I understand SRA...

Both link to same page.

I understand SRA run, they have ID as SRR.

For eg: take this case.
http://www.ncbi.nlm.nih.gov/sra?term=SRA028225
http://www.ncbi.nlm.nih.gov/sra?term=SRA028192...
Forum: Bioinformatics 11-17-2011, 02:40 AM
Replies: 15
Views: 6,544
Posted By ersgupta
@vadim... thnx a lot... This is wht I was...

@vadim... thnx a lot...

This is wht I was looking for. But in this also one issue is that not every SRA id is having study.xml, but its ok. I can live with that. :)
Forum: Bioinformatics 11-16-2011, 09:26 PM
Replies: 15
Views: 6,544
Posted By ersgupta
Thanx for the reply. I have checked it but...

Thanx for the reply.

I have checked it but it doesnt contain the information I want i.e. study abstract and description. It only contains IDs, which I already have.

I am trying few other...
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