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Search: Posts Made By: hsmart
Forum: Bioinformatics 07-08-2013, 06:54 AM
Replies: 4
Views: 1,067
Posted By hsmart
Thank you so much for your help. It worked...

Thank you so much for your help. It worked perfectly fine.
Forum: Bioinformatics 07-05-2013, 12:43 PM
Replies: 4
Views: 1,067
Posted By hsmart
Thanks for looking into it. We are using Illumina...

Thanks for looking into it. We are using Illumina platform to generate data. I have used several packages (i.e., BWA, asSeq in R and samtools) so basically some of the reads were trimmed. Is there...
Forum: Bioinformatics 07-03-2013, 02:11 PM
Replies: 4
Views: 1,067
Posted By hsmart
Samtool error

Hi All,
I am getting following error with SAMtools while converting .sam file to .bam file.
samtools view -bt hg19.fa Input.sam -o Output.bam
Parse error at line 103686571: sequence and quality...
Forum: Bioinformatics 03-29-2011, 07:26 AM
Replies: 0
Views: 1,221
Posted By hsmart
CEAS error

Hi All,

I am getting error message with following command:

ceas --name=htert_polii -g hg19.refGene -b summary-FDR1E-3.bed

Traceback (most recent call last):
File "/home/hemang/bin/ceas",...
Forum: Bioinformatics 03-03-2011, 07:49 AM
Replies: 3
Views: 2,985
Posted By hsmart
Hi Nico, Thanks for your detail response. I...

Hi Nico,

Thanks for your detail response. I tried to use samtools and bedtools to convert .sam files to .bed files but I used human genomes 19 as reference. But I believe it might be better to use...
Forum: Bioinformatics 03-02-2011, 07:36 AM
Replies: 3
Views: 2,985
Posted By hsmart
miRNAkey

Hi All,

I am referring to your publication "miRNAkey: a software for microRNA deep sequencing analysis" in Bioinformatics.

I have few questions regarding the output of the miRNAkey....
Forum: Bioinformatics 02-28-2011, 07:10 AM
Replies: 1
Views: 2,508
Posted By hsmart
miRExpress

Hi All,

We like to use miRExpress software (http://mirexpress.mbc.nctu.edu.tw/) for our microRNA-seq data. I tried to run the example file however I am getting error as Segmentation fault with...
Forum: Bioinformatics 02-01-2011, 12:12 PM
Replies: 3
Views: 2,764
Posted By hsmart
Hi, Thank you so much for your help. It...

Hi,

Thank you so much for your help.
It worked perfectly with
awk '{print "chr"$0}' Homo_sapiens.GRCh37.60.gtf | sed 's/chrMT/chrM/g' > hg19.ensembl-for-tophat.gtf

I really appriciate your...
Forum: Bioinformatics 02-01-2011, 10:43 AM
Replies: 0
Views: 1,249
Posted By hsmart
Myrna error

Dear All,

Myrna software: http://bowtie-bio.sourceforge.net/myrna/index.shtml
I am trying to use Myrna software to analyze RNA-seq data from two cell-lines. We repeated experiments twice for...
Forum: Bioinformatics 02-01-2011, 08:00 AM
Replies: 3
Views: 2,764
Posted By hsmart
Dear All, I am trying to use cufflinks to...

Dear All,

I am trying to use cufflinks to analyze RNA-seq data from two cell-lines. I used following commands:
cuffcompare -i ~/Cufflink_files.txt -r ~/Homo_sapiens.GRCh37.60.gtf -R -p...
Forum: Bioinformatics 02-01-2011, 07:53 AM
Replies: 1
Views: 1,491
Posted By hsmart
Dear All, Myrna software:...

Dear All,

Myrna software: http://bowtie-bio.sourceforge.net/myrna/index.shtml
I am trying to use Myrna software to analyze RNA-seq data from two cell-lines. We repeated experiments twice for...
Forum: Literature Watch 11-24-2010, 02:08 PM
Replies: 1
Views: 4,494
Posted By hsmart
Dear All, We generated ChIP-seq and RNA-seq...

Dear All,

We generated ChIP-seq and RNA-seq data few cell-lines. I want to visualize these data in UCSC Genome Browser. How can I make appropriate files similar to ENCODE density plots for...
Forum: Bioinformatics 02-14-2010, 05:29 PM
Replies: 3
Views: 4,481
Posted By hsmart
UCSC .bed file

Hi All,

We have created a .bed file for UCSC browser. However, we would like to change score range from 0 to 20 instead of 0 to 1000. Can you please guild me how to do it?

Here is the more...
Forum: Bioinformatics 02-14-2010, 05:26 PM
Replies: 1
Views: 1,101
Posted By hsmart
Cufflinks

Hi All,

I am trying use Cufflinks with output of tophat. The command is as follow:

cufflinks HTERT_tophat_accepted_hits.sam.sorted -G Homo_sapiens.GRCh37.56.gtf -L HTERT

However, Cufflinks...
Forum: Bioinformatics 12-09-2009, 05:51 AM
Replies: 0
Views: 1,198
Posted By hsmart
MosaikAligner

Hi All,

I am trying to use MosaikAligner with following command.
MosaikAligner -in s_1_sequence.dat -ia hg19_ref.dat -m unique -mm 2 -hs 11 -act 20 -out s_1_sequence_aligned.dat -rur...
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