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Forum: RNA Sequencing 10-21-2011, 01:29 PM
Replies: 0
Views: 1,637
Posted By nimmi
scripture output

We did RNA-seq on 5 cases and 5 controls. Following the documentation given on scripture website I got some results for Chr1. Below are few lines from the output. There are a total of 64K rows for...
Forum: Bioinformatics 01-12-2011, 11:59 AM
Replies: 0
Views: 1,640
Posted By nimmi
samtools/bcftools problem?

Hi,

I have exome data (single end reads from SoLiD). I am trying to call SNPs using bcftools with the following command

>bcftools view -vcG *.bcf >*.vcf

The *.vcf file only has indels...
Forum: Bioinformatics 01-05-2011, 08:40 AM
Replies: 6
Views: 1,773
Posted By nimmi
Thanks Nils for the perl script. Just to...

Thanks Nils for the perl script.

Just to summarize........I converted *.sam file to *.fastq using PICARD and this fastq file was in nucleotide space. When I ran localalign in bfast I got the...
Forum: Bioinformatics 01-04-2011, 01:44 PM
Replies: 6
Views: 1,773
Posted By nimmi
Thanks Nils for your response. Here's a few lines...

Thanks Nils for your response. Here's a few lines from my *.sam file:

1462_1719_1204_F3 0 chr1 10006 0 50M * 0 0 ...
Forum: Bioinformatics 01-04-2011, 11:00 AM
Replies: 6
Views: 1,773
Posted By nimmi
Here are the list of files in my directory: ...

Here are the list of files in my directory:

03C14605A.fastq
chr_all.fa
chr_all.fa.cs.brg
chr_all.fa.cs.1.1.bif
chr_all.fa.nt.brg
03C14605A_bfastMatches_hg19.bmf

Here's the command I used...
Forum: Bioinformatics 01-03-2011, 11:29 AM
Replies: 6
Views: 1,773
Posted By nimmi
bfast localalign error

Hi,

I am trying to map exome data using bfast. I received *.sam files from our collaborates. Here's a summary of my method:

1. Converted *.sam to *.fastq using PICARD
2. Converted hg19.fa...
Forum: Bioinformatics 12-01-2010, 08:15 AM
Replies: 12
Views: 7,300
Posted By nimmi
Sorry it was a typo in my previous post. Here's...

Sorry it was a typo in my previous post. Here's the command:

cuffdiff -o cuffDiffOutput ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam
Forum: Bioinformatics 11-30-2010, 06:30 PM
Replies: 12
Views: 7,300
Posted By nimmi
It stops immediately giving a segmentation fault...

It stops immediately giving a segmentation fault error
Forum: Bioinformatics 11-30-2010, 11:32 AM
Replies: 12
Views: 7,300
Posted By nimmi
Hi, Thank you for your response. Here is...

Hi,
Thank you for your response.

Here is the command that I am using:

cuffdiff -o ucsc_refseq.gtf sample1_accepted_hits.sam sample2_accepted_hits.sam

Each *.sam file is ~50G so not sure if...
Forum: Bioinformatics 11-30-2010, 10:45 AM
Replies: 12
Views: 7,300
Posted By nimmi
I am also encountering the same problem. It would...

I am also encountering the same problem. It would be great if someone can suggest a solution to this.

Thanks in advance.
Forum: Bioinformatics 11-19-2010, 02:26 PM
Replies: 3
Views: 3,429
Posted By nimmi
understanding HTSeq counts

Hi,

I ran HTSeq on a *.sam file using RefSeq genes GTF file. I got counts for each transcript and would like to understand how exactly these counts were generated. Does HTSeq count a read...
Forum: RNA Sequencing 10-28-2010, 12:24 PM
Replies: 2
Views: 2,379
Posted By nimmi
tophat with mixed paired end reads

Hi,

I have a file with mixed paired end reads (50bp and 70bp). My insert size is 400bp. Did anyone try running tophat with mixed paired end reads? If so, what would be the tophat -r option...
Forum: RNA Sequencing 10-25-2010, 11:28 AM
Replies: 0
Views: 1,657
Posted By nimmi
help with bowtie-inspect

Hi,

In order to convert the bedgraph file to bigwig file format I need chrom.sizes file. I downloaded pre-built index files from Tophat website to run Tophat. I tried to use bowtie-inspect...
Forum: Bioinformatics 09-15-2010, 11:54 AM
Replies: 0
Views: 948
Posted By nimmi
convert reads

Hi,

I would like to convert transcriptome data - *.export files to *.fastq format. What programs are best for file format conversions?

Thank you very much.
Nirmala
Forum: Sample Prep / Library Generation 09-03-2010, 08:43 AM
Replies: 3
Views: 6,349
Posted By nimmi
Agilent SureSelect Human All Exon 50MB kit vs 38MB kit

Hi,

Did anyone use Agilent sureselect Human all exon 50MB kit? If so, could you please post pros and cons of this kit? How does it perform compared to Sureselect 38 MB?

Thanks,
Nirmala
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