SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: bjchen
Forum: Bioinformatics 07-03-2013, 12:28 PM
Replies: 0
Views: 2,589
Posted By bjchen
interpret GC bias metrics from Picard

Hi,

I am working with a RNA-seq dataset (human samples), and am generating many "metrics" from Picard to check quality. Picard has a tool "CollectGCBiasMetrics", which calculate the normalized...
Forum: Bioinformatics 07-10-2012, 02:35 PM
Replies: 0
Views: 1,701
Posted By bjchen
cuffmerge reports new transcripts?

Hi,

I ran cufflinks 2.0.2 on our data (7 samples in total) and then used cuffmerge to merge transcripts. However, I found cuffmerge reports transcripts that are not included in transcripts.gtf of...
Forum: Bioinformatics 06-28-2012, 11:07 AM
Replies: 5
Views: 2,478
Posted By bjchen
What if you change your test.sh to just take one...

What if you change your test.sh to just take one .fq file at a time and you pass the file name to test.sh in the for-loop of your initial script?
Forum: Bioinformatics 04-11-2012, 12:22 PM
Replies: 0
Views: 1,450
Posted By bjchen
Problems with Bam files from Tophat

Hi,

I have some troubles with bam files output from tophat and I hope someone here can help me.

1. I have finished running tophat (1.4.1) using UCSC hg19, WITHOUT "--no-sort-bam". But I found...
Forum: Bioinformatics 02-12-2012, 07:56 PM
Replies: 5
Views: 4,908
Posted By bjchen
Setting -Djava.io.tmpdir seems to work! Thanks a...

Setting -Djava.io.tmpdir seems to work! Thanks a lot!!
Forum: Bioinformatics 02-12-2012, 04:26 PM
Replies: 5
Views: 4,908
Posted By bjchen
Uh... I have about 500G on the drive where I have...

Uh... I have about 500G on the drive where I have GATK and my bam files. Each of my bam file is only about 1G. So I don't think that drive does not have enough space (please correct me if I am...
Forum: Bioinformatics 02-12-2012, 01:23 PM
Replies: 5
Views: 4,908
Posted By bjchen
GATK: unable to write data to BAM schedule file

Hi,

I am trying to use UnifiedGenotyper in GATK, but encountered the following error message (below). Does anyone know how to deal with this? I check my quota on the directory of the bam file and...
Forum: Bioinformatics 02-10-2012, 07:05 AM
Replies: 2
Views: 2,020
Posted By bjchen
That's what I guessed, although still got...

That's what I guessed, although still got confused by the "+" in the "1.3+"...
Thanks!
Forum: Bioinformatics 02-09-2012, 11:21 AM
Replies: 2
Views: 2,020
Posted By bjchen
question about samtools mpileup -6

Hi,

Can anyone please tell me when to use this option? I am a bit confused about this. I have sequence data with Illumina 1.8 encoding and have aligned them to generate bam files. In the...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 03:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO