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Forum: Bioinformatics 05-14-2015, 02:48 PM
Replies: 4
Views: 2,177
Posted By mediator
Open the VCF file in the latest version of IGV,...

Open the VCF file in the latest version of IGV, then zoom out until your desired interval. You can then save the image as PNG or SVG.
Forum: Bioinformatics 04-13-2015, 09:47 AM
Replies: 2
Views: 3,301
Posted By mediator
That genome is not sorted in karyotypic order ...

That genome is not sorted in karyotypic order
chr10 130694993 7 50 51
chr11 122082543 133308907 50 51
chr12 120129022 257833108 50 51
chr13 120421639 380364718 50 51...
Forum: Bioinformatics 04-13-2015, 09:07 AM
Replies: 2
Views: 3,301
Posted By mediator
mini tutorial: build reference mouse genome and SNP for GATK

GATK is a standard tool for calling SNPs however their authors did not provide any reference genomes or reference SNPs for non-human organism, such as mouse. Here is my quick tutorial for building a...
Forum: Bioinformatics 10-14-2014, 12:19 PM
Replies: 0
Views: 914
Posted By mediator
Help with PathSeq running

Hi,
New to pathSeq and I have to questions about running PathSeq.
1. In the cluster.config file, how do I set the directory for S3CMD? My system administror install the S3CMD for me, not sure if I...
Forum: Bioinformatics 02-13-2013, 01:57 PM
Replies: 6
Views: 6,294
Posted By mediator
OP, bwa sampe is a very slow step. It took my...

OP, bwa sampe is a very slow step. It took my cluster more than two days to convert the two sai files into one sam file. My reads are 100 million in size.
Forum: Bioinformatics 03-25-2012, 02:27 PM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, I tried to import the bed files as...

Hi Simon,
I tried to import the bed files as annotated track but Seqmonk could not recognize those files. I just import them as BED files, and quantify by using "RPKM calculation for RNA-Seq data"....
Forum: Bioinformatics 03-25-2012, 11:51 AM
Replies: 7
Views: 3,909
Posted By mediator
@kjlee Thanks for the advice! I already use MeV...

@kjlee
Thanks for the advice! I already use MeV for microarray. Pretty handy. Let's see how RNA-Seq data goes with MeV.
Forum: Bioinformatics 03-22-2012, 04:30 PM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, Thanks for the help! Will try that.

Hi Simon,
Thanks for the help! Will try that.
Forum: Bioinformatics 03-22-2012, 01:49 PM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, For bed file (generated by Scripture,...

Hi Simon,
For bed file (generated by Scripture, from RNA-Seq data), which quantification pipeline would you recommend? I am trying to compare bed files between patients and healthy controls in order...
Forum: Bioinformatics 03-19-2012, 09:51 AM
Replies: 17
Views: 6,284
Posted By mediator
Does anyone know if Scripture accept BAM as input...

Does anyone know if Scripture accept BAM as input files? Thanks.
Forum: General 03-06-2012, 09:49 AM
Replies: 5
Views: 2,109
Posted By mediator
Because it is more profitable and less risk to...

Because it is more profitable and less risk to acquire an existing technology than develop a new one.
Forum: Bioinformatics 03-05-2012, 09:42 PM
Replies: 0
Views: 2,583
Posted By mediator
samtools sort bam file error: generate non-existent file

Hi,
The following is the shell script I wrote to use samtools for sorting bam files. The bam files are from pair end Tophat alignment.


The script seemed run OK. But when I do ls -l under the...
Forum: Bioinformatics 03-05-2012, 09:19 AM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, Do you know if SeqMonk can show the...

Hi Simon,
Do you know if SeqMonk can show the exact base pairs for each reads? It will be very helpful for detecting indels and de novo mutation. Thank you!
Forum: Bioinformatics 02-25-2012, 04:07 PM
Replies: 313
Views: 109,607
Posted By mediator
Thank you Simon!

Thank you Simon!
Forum: Bioinformatics 02-24-2012, 11:15 AM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, That advanced course is really...

Hi Simon,
That advanced course is really helpful, thanks! Do you know when use difference filter to identify differentially expressed genes, what is the appropriate interval for RNA-Seq experiments?...
Forum: Bioinformatics 02-23-2012, 08:09 AM
Replies: 2
Views: 1,563
Posted By mediator
@pbluescript Will try that, thanks!

@pbluescript
Will try that, thanks!
Forum: Bioinformatics 02-22-2012, 08:07 AM
Replies: 2
Views: 1,563
Posted By mediator
Tophat 1.4.1 paired end alignment error -11 healp

Hi All,
I was running Tophat1.4.1 to do a pair-end alignment but got err=-11. Here is the command I used:

module load bowtie/0.12.7
module load tophat/1.4.1
tophat -m 2 -p 16 -r 210 -o <output...
Forum: Bioinformatics 02-01-2012, 10:12 AM
Replies: 7
Views: 3,909
Posted By mediator
@chadn737 Thanks! @Richard Finney I used...

@chadn737
Thanks!
@Richard Finney
I used Seqmonk to generate RPKM , results are by exons but can be averaged to by genes. I would like to visualize in a hierarchical clustered heat map, like many...
Forum: General 02-01-2012, 10:07 AM
Replies: 1
Views: 13,713
Posted By mediator
RNA Seq work shop, conferences in 2012?

Hi All,
Are there any workshops or conferences related to RNA Seq, or just NGS in general this year? Didn't find any in Keystone Symposia nor Gorden Research Conferences. And still no update for...
Forum: Bioinformatics 02-01-2012, 09:57 AM
Replies: 7
Views: 3,909
Posted By mediator
Identify and visualize differentially expressed genes from RNA-Seq data?

Hi All,
I have aligned RNA Seq data for four healthy controls and four patients, in bam format. Then I made a table for RPKM for all the genes. Now how do I quickly identify and visualize those...
Forum: Bioinformatics 02-01-2012, 09:48 AM
Replies: 5
Views: 4,153
Posted By mediator
You can just do two rounds of rRNA removal. I've...

You can just do two rounds of rRNA removal. I've used invitrogen's ribominus, cleared more than 90% of rRNA in first round (confirmed by real time PCR of 18s).
Forum: Bioinformatics 01-31-2012, 09:41 AM
Replies: 3
Views: 2,015
Posted By mediator
@jbrwn Thanks! Hope that improves my alignment...

@jbrwn
Thanks! Hope that improves my alignment rate.
Forum: Bioinformatics 01-31-2012, 09:25 AM
Replies: 3
Views: 2,015
Posted By mediator
Tophat paired end alignment help: comma or blank to separate two pairs?

Hi All,
I am using the current command to run a PE alignment in Tophat:
$ tophat -p 4 -m 2 -r 200 /index/hg19 /data/raw/N1_1.fa,N1_2.fa

my question is, both N1_1.fa and N1_2.fa are the paired...
Forum: Bioinformatics 01-30-2012, 11:36 AM
Replies: 313
Views: 109,607
Posted By mediator
Hi Simon, I am using the Seqmonk to analyze my...

Hi Simon,
I am using the Seqmonk to analyze my RNA Seq data right now. It's very straightforward and intuitive. Just have a question, after I used the quantitation pipeline to perform RPKM...
Forum: Bioinformatics 12-14-2011, 08:55 PM
Replies: 514
Views: 223,048
Posted By mediator
Yes, my data was RNA-Seq. Thanks for the advice!...

Yes, my data was RNA-Seq. Thanks for the advice! Do you think -X will help?
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