Forum: Bioinformatics
07-08-2013, 06:54 AM
|
|
Replies: 4
Views: 1,080
|
|
Forum: Bioinformatics
07-05-2013, 12:43 PM
|
|
Replies: 4
Views: 1,080
|
|
Forum: Bioinformatics
07-03-2013, 02:11 PM
|
|
Replies: 4
Views: 1,080
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: 1,242
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: 3,012
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: 3,012
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: 2,560
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: 2,789
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: 1,262
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: 2,789
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: 1,505
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: 4,535
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: 4,519
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: 1,108
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: 1,222
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...
|
