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Forum: Bioinformatics 08-07-2014, 06:00 PM
Replies: 0
Views: 1,297
Posted By newbietonextgen
beagle input format

Hello All,

I am trying to impute using beagle 4 and was wondering how the vcf file has to be formatted. I did get the reference or phase file formatted and am having trouble with imputation...
Forum: Bioinformatics 09-25-2013, 07:54 AM
Replies: 2
Views: 1,614
Posted By newbietonextgen
True to some extent as i have tried GSNAP vs...

True to some extent as i have tried GSNAP vs Tophat vs CLC. But what baffles me are the differences in numbers. What would happen if you are working on depth of coverage data and how would one...
Forum: Bioinformatics 09-24-2013, 06:18 PM
Replies: 26
Views: 15,699
Posted By newbietonextgen
I will look into the white paper. Is there a way...

I will look into the white paper. Is there a way to look into accuracy of alignment, as far as metrics etc. Any suite that can be used or work flow..

Thanks
newbie
Forum: Bioinformatics 09-24-2013, 01:05 PM
Replies: 2
Views: 1,614
Posted By newbietonextgen
CLC vs tophat: differences is alignment?

Hi

I have been using CLC for sometime and was wondering if any one has compared metrics between CLC and other aligners.

I found something interesting and wanted to know if anybody has...
Forum: Bioinformatics 09-24-2013, 01:03 PM
Replies: 26
Views: 15,699
Posted By newbietonextgen
Hi I have been using CLC for sometime and...

Hi

I have been using CLC for sometime and was wondering if any one has compared metrics between CLC and other aligners.

I found something interesting and wanted to know if anybody has...
Forum: Bioinformatics 09-05-2013, 08:46 AM
Replies: 28
Views: 5,353
Posted By newbietonextgen
GMAP and HTseq problems

I use GMAP to align my RNA-seq and then I use HT-Seq to get the counts. When i run the HTseq count script, it always complains of the sam file not being sorted.

I have used from picard tools,...
Forum: Bioinformatics 08-10-2013, 06:59 PM
Replies: 0
Views: 710
Posted By newbietonextgen
Wink GATK ? How to out put all read numbers

Hi,

I have a question regarding GATK. I am trying to get SNP calls and the number of reads associated with it (AD). When i look at the data, the number reads is no greater than 99 either for...
Forum: Bioinformatics 06-14-2013, 05:25 AM
Replies: 6
Views: 2,770
Posted By newbietonextgen
You need both the files (fasta and .dict) to be...

You need both the files (fasta and .dict) to be present in the same folder/location.

Picard tools (http://picard.sourceforge.net) will help you with adding RG groups to your bam files. Use the...
Forum: Bioinformatics 06-14-2013, 05:19 AM
Replies: 1
Views: 1,499
Posted By newbietonextgen
a little bit of digging around and i see that an...

a little bit of digging around and i see that an error is also posted...

Error: Exception: Cannot read past the end of the alignment's sequence.


So what does this mean? Any ideas?
Forum: Bioinformatics 06-12-2013, 09:01 AM
Replies: 1
Views: 1,499
Posted By newbietonextgen
Freebayes 0.9.9 problems

Hello All,

I am trying to run freebayes version 0.9.9 and am having problems. I am used pervious versions and never encountered these problems.

The command is use:

freebayes -XuiP 0.01 -f...
Forum: Bioinformatics 06-12-2013, 08:38 AM
Replies: 6
Views: 2,770
Posted By newbietonextgen
Would be easy to run the jar file than running on...

Would be easy to run the jar file than running on the Galaxy. You need to have a .dict (dictionary) file of the fasta file used for alignment. Picards tools can be used to make .dict file. You can...
Forum: Bioinformatics 07-16-2012, 05:47 PM
Replies: 2
Views: 1,967
Posted By newbietonextgen
Shrimp worked well. I thinks its some program...

Shrimp worked well. I thinks its some program down the line that goofed the results. For now i just am using a different approach (Freebayes) and no problems yet..
Forum: Bioinformatics 07-11-2012, 08:25 AM
Replies: 2
Views: 1,967
Posted By newbietonextgen
Who is the culprit? Picard, Samtools or GATK?

hi,

I am using RNA-Seq data and my work flow is below..and am having trouble with BAM file

Single end fastq->Shrimp alignment->sam file->changed to BAM using Samtools->added read groups using...
Forum: Bioinformatics 07-11-2012, 08:13 AM
Replies: 6
Views: 4,286
Posted By newbietonextgen
what version if you can add? I used 2.0.0.4 and...

what version if you can add? I used 2.0.0.4 and my SAM/BAM files were not compatible with GATK. Same data aligned using SHRIMP, no problem works like a charm..
Forum: Bioinformatics 07-11-2012, 08:00 AM
Replies: 6
Views: 4,286
Posted By newbietonextgen
I am having the same problem. RNA-seq data. Have...

I am having the same problem. RNA-seq data. Have tried even Splice map and the sam files are just crap cannot use it down stream. Did you find a way around this? If so kindly, let me know.
Forum: Bioinformatics 07-09-2012, 04:43 PM
Replies: 7
Views: 3,066
Posted By newbietonextgen
thanks for the help. Yes, i do have two...

thanks for the help. Yes, i do have two populations that i need to call the SNPs. I am sure your method works, but i will keep it as an last resort. But its a such as shame that such a useful tool is...
Forum: Bioinformatics 07-09-2012, 04:29 PM
Replies: 7
Views: 3,066
Posted By newbietonextgen
But i was looking into the protocol and it calls...

But i was looking into the protocol and it calls for ideally not doing it unless you are an expert..moreover dos it not help in the validation and recalibration steps?
Forum: Bioinformatics 07-09-2012, 03:51 PM
Replies: 7
Views: 3,066
Posted By newbietonextgen
I need to call SNPs from a population to look at...

I need to call SNPs from a population to look at ASE. I have had used GATK before but with the change in format and inout files, its tough to recreate it...
Forum: Bioinformatics 07-09-2012, 03:35 PM
Replies: 7
Views: 3,066
Posted By newbietonextgen
GATK with non-model organism (Help with making SNP VCF file))

Hi

Has any one tried using GATK with a non-model organism? If so kindly, would you tell me the format of the VCF files you are using? I was reading few posts at the GATK forum and got details...
Forum: Bioinformatics 07-01-2012, 01:51 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
also i have tried other software like Splice map...

also i have tried other software like Splice map and even the SAM file when converted to BAM doesn't pass through GATK BAM norm. SO strange. Shrimp alignment works fine...why is there so much...
Forum: Bioinformatics 06-29-2012, 10:40 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
It's sanger quality (1.9 Illumina pipeline)

It's sanger quality (1.9 Illumina pipeline)
Forum: Bioinformatics 06-29-2012, 08:41 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
samtools view file.bam | grep...

samtools view file.bam | grep "HWI-ST913:105:C0EYJACXX:5:1304:11235:16705" > bad_read.sam

Output. looks like there is * instead of quality score. Now have to check fastq file....
...
Forum: Bioinformatics 06-29-2012, 08:08 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
Tophat: 2.0.0.4 the run command i used.. ...

Tophat: 2.0.0.4

the run command i used..

./tophat -p 4 -G /home/sudeep/work/6-20-12/Gallus_gallus.WASHUC2.67.gtf -o /home/sudeep/work/6-20-12/layers/Infected/1_4I...
Forum: Bioinformatics 06-29-2012, 07:08 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
I did find something. This problem is only...

I did find something.

This problem is only with Tophat based BAM files. I have a SHRIMP based BAM alignment and GATK works like a charm. Can any one shed some information as to why?
Forum: Bioinformatics 06-29-2012, 05:36 AM
Replies: 9
Views: 2,711
Posted By newbietonextgen
Unhappy GATK BAM error

Hi

I am having trouble with GATK ability to read my BAM files. THe BAM were created using tophat 2.0.0.4 and I used AddandReplaceReadGroups from Picard tools to do it. The code used was

java...
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