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Forum: Bioinformatics 07-31-2012, 01:48 PM
Replies: 1
Views: 1,460
Posted By caddymob
Check out CalculateHsMetrics from Picard: ...

Check out CalculateHsMetrics from Picard:
http://picard.sourceforge.net/command-line-overview.shtml#CalculateHsMetrics
Forum: RNA Sequencing 07-31-2012, 01:12 PM
Replies: 9
Views: 7,720
Posted By caddymob
I consistently see it skipping these in humans: ...

I consistently see it skipping these in humans:

21:38435145-45747259 Warning: Skipping large bundle.
6:126102306-130463972 Warning: Skipping large bundle.

The chr21 locus is huge and part of...
Forum: Bioinformatics 07-23-2012, 10:40 AM
Replies: 1
Views: 1,496
Posted By caddymob
Turns out this was due to an upgrade to our...

Turns out this was due to an upgrade to our isilon NFS disk... Rebooting machines fixed the error. Very strange, but moving on...
Forum: Bioinformatics 07-19-2012, 08:32 AM
Replies: 1
Views: 1,496
Posted By caddymob
Unhappy tophat2 splice sequence has more than 2^32-1 characters

Hello,

I have 60 samples that I've tried on tophat2 and about half have all failed at Indexing splices saying "Error: Reference sequence has more than 2^32-1 characters".

Anyone else get this...
Forum: Bioinformatics 06-13-2012, 09:17 AM
Replies: 22
Views: 7,726
Posted By caddymob
Yes - I have the same error with a FAILED at...

Yes - I have the same error with a FAILED at tophat_reports. Tried on 2 different genomes (human and rat). I have standard 100bp paired reads. Also tried the unannounced tophat 2.0.4...
Forum: Bioinformatics 04-28-2012, 06:47 AM
Replies: 4
Views: 2,043
Posted By caddymob
I'm having the same issue with tophat2. I just...

I'm having the same issue with tophat2. I just posted over here: http://seqanswers.com/forums/showpost.php?p=72066&postcount=4
Forum: Bioinformatics 04-28-2012, 06:43 AM
Replies: 13
Views: 9,038
Posted By caddymob
Exclamation I have the same issue with tophat2, using...

I have the same issue with tophat2, using bowtie2. Some reads have qualities, some just have "*" in the quality field. Here are 2 examples, 1st with no quality, 2nd with quality:

...
Forum: Bioinformatics 04-05-2012, 10:01 AM
Replies: 4
Views: 3,092
Posted By caddymob
I had this same error and it was because a bug in...

I had this same error and it was because a bug in my script had the wrong path to dbSNP135.vcf. Your log seems to show that dbSNP, hapmap and omni were loaded OK, but I noticed some weird chromosome...
Forum: Bioinformatics 10-18-2011, 09:42 AM
Replies: 1
Views: 1,948
Posted By caddymob
using the biomaRt package in R makes this kind of...

using the biomaRt package in R makes this kind of thing really easy with ensembl:

http://www.bioconductor.org/packages/2.2/bioc/html/biomaRt.html
Forum: Bioinformatics 05-13-2011, 06:50 PM
Replies: 89
Views: 53,789
Posted By caddymob
Correct, they're rat RNA-seq. Glad they worked...

Correct, they're rat RNA-seq. Glad they worked anyway :)
Forum: Bioinformatics 05-12-2011, 10:30 AM
Replies: 89
Views: 53,789
Posted By caddymob
Couple test CASVA 1.8 fastqs with 400 reads for...

Couple test CASVA 1.8 fastqs with 400 reads for read 1 and read 2 attached, no QC filtering applied. Hope this helps!
Forum: Bioinformatics 05-11-2011, 02:04 PM
Replies: 89
Views: 53,789
Posted By caddymob
I missed that, but yes, very good point!

I missed that, but yes, very good point!
Forum: Bioinformatics 05-11-2011, 11:48 AM
Replies: 89
Views: 53,789
Posted By caddymob
@sparks -- this is just like the 0/1 (fail/pass)...

@sparks -- this is just like the 0/1 (fail/pass) in the last field old qseq files. The problem, to my knowledge is that all reads are output to the fastq.qz. Y means failed QC. Seems backwards I...
Forum: Bioinformatics 05-11-2011, 11:32 AM
Replies: 31
Views: 10,927
Posted By caddymob
Cole, I am having the same problem with...

Cole, I am having the same problem with cuffcompare. I wonder if this is related to my previous post regarding problems with cuffmerge?

This is using ensembl Homo_sapiens.GRCh37.61.
...
Forum: Bioinformatics 05-10-2011, 03:43 PM
Replies: 31
Views: 10,927
Posted By caddymob
Thanks for all your awesome work Cole and team! ...

Thanks for all your awesome work Cole and team!

cuffmerge is an awesome new feature, particularily when cuffdiff is on tap. Thanks for adding this. I found that using the stats.combined.gtf GTFs...
Forum: Bioinformatics 12-20-2010, 08:08 AM
Replies: 278
Views: 97,101
Posted By caddymob
next steps...

Maybe .. our system was under high load and the time and the infinband links on the LUSTRE file system may have been saturated, compounding the problem. Nevertheless I have been warned not to try...
Forum: Bioinformatics 12-15-2010, 06:24 PM
Replies: 278
Views: 97,101
Posted By caddymob
I made a lot of people angry with Ray today....

Hi seb567,

So, I had Ray 1.2.0 installed on our cluster, complied with the same with Intel Compiler. The job starts to run, then is crashing.... Apparently today I took down 32 compute nodes...
Forum: Bioinformatics 11-29-2010, 10:31 AM
Replies: 278
Views: 97,101
Posted By caddymob
Many thanks seb567! I had to have my IT...

Many thanks seb567!

I had to have my IT department compile and install Ray on our cluster and did not notice they used the old version of Ray. Thanks for pointing this out. I have requested the...
Forum: Bioinformatics 11-29-2010, 09:30 AM
Replies: 278
Views: 97,101
Posted By caddymob
Question processes aborted

Really excited to try out Ray! I first tried to grab the example datasets, but the links are dead.. getting a 550 error, no such file..

So then I went ahead and tried to assemble my own genome of...
Forum: Bioinformatics 11-11-2010, 01:54 AM
Replies: 38
Views: 10,082
Posted By caddymob
Ok, you have a sam, not a bam? Then just edit the...

Ok, you have a sam, not a bam? Then just edit the sam header directly. Then samtools import the sam to make it a bam. Should be good to go.
Forum: Bioinformatics 11-11-2010, 01:25 AM
Replies: 38
Views: 10,082
Posted By caddymob
How are you seeing the header then that you...

How are you seeing the header then that you posted previously?
Forum: Bioinformatics 11-11-2010, 01:14 AM
Replies: 10
Views: 5,619
Posted By caddymob
Thanks frozenlyse -- I looked at myrna when it...

Thanks frozenlyse -- I looked at myrna when it first came out and didn't like the amazon cloud stuff, since this isn't an option for me. However, I admit that I did not look closely at it, which I...
Forum: Bioinformatics 11-11-2010, 12:19 AM
Replies: 38
Views: 10,082
Posted By caddymob
Does your header only have the one @HD line? You...

Does your header only have the one @HD line? You need the full header... Seems like picard should error out on this, but maybe not?

You can do "samtools view -H my.bam > header.txt" then modify...
Forum: Bioinformatics 11-10-2010, 06:26 AM
Replies: 10
Views: 5,619
Posted By caddymob
Thanks GKM. This is HiSeq data so I am getting...

Thanks GKM. This is HiSeq data so I am getting upwards of 110 million paired reads (so 220+ million single end reads) in a single lane, and each lane is a single sample... Kinda funny, now we are...
Forum: Bioinformatics 11-09-2010, 07:07 PM
Replies: 38
Views: 10,082
Posted By caddymob
@urchgene - you can use Picard ReplaceSamHeader,...

@urchgene - you can use Picard ReplaceSamHeader, paste the modified header below into a txt file to fix up the header... I did this before tophat was fixed and it worked for downstream stuff :)

...
Showing results 1 to 25 of 36

 


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