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Search: Posts Made By: myrna
Forum: Bioinformatics 09-26-2013, 08:15 AM
Replies: 2
Views: 1,972
Posted By myrna
Novoalign inappropriately softclipping?

I have downloaded some exome data that appears to have been aligned using Novoalign
I determined this from the header:

@PG ID:novoalign VN:V2.06.09 CL:novoalign -c 16 -o SAM -o SoftClip -r Random...
Forum: General 12-05-2012, 10:35 AM
Replies: 2
Views: 6,319
Posted By myrna
I am in a similar situation. Did you ever...

I am in a similar situation. Did you ever determine if the reagent is the same in both kits (i.e. is HS dye + HS buffer the same as the picogreen reagent)? Someone told me the concentrations may be...
Forum: Pacific Biosciences 09-16-2011, 12:29 PM
Replies: 10
Views: 5,741
Posted By myrna
Out of interest, how long do you have to run the...

Out of interest, how long do you have to run the machine to yield an average read length of 1.5-2kb?
Forum: Pacific Biosciences 09-16-2011, 11:14 AM
Replies: 10
Views: 5,741
Posted By myrna
Are there even recent company specs posted...

Are there even recent company specs posted anywhere?
Forum: Bioinformatics 06-18-2011, 10:48 AM
Replies: 7
Views: 5,798
Posted By myrna
Thanks Nils. Does VALIDATION_STRINGENCY=SILENT...

Thanks Nils.
Does VALIDATION_STRINGENCY=SILENT apply to running SRMA or will this only work for Picard tools? In other words, I'm wondering if FixMateInformation is a prerequisite for running SRMA...
Forum: Bioinformatics 06-17-2011, 03:43 PM
Replies: 7
Views: 5,798
Posted By myrna
FixMateInformation complains about incorrect mate pair information

I was trying to use SRMA to perform local realignment of my RNA-seq data. It complained about some reads having bad mate information. I think it is because the mates of some of my reads mapped to...
Forum: Bioinformatics 03-05-2009, 07:34 PM
Replies: 292
Views: 151,929
Posted By myrna
samtools index

Have you tried samtools view foo.bam?

If you get the sam alignments back, then all should be well. I believe you get a warning if the .bam file is unsorted, but perhaps you should try this if you...
Forum: Bioinformatics 03-05-2009, 07:17 PM
Replies: 292
Views: 151,929
Posted By myrna
samtools import

samtools import is for making a .bam file from a .sam file. Why are you attempting to run this command on a .bam file?
Forum: Bioinformatics 02-18-2009, 08:52 AM
Replies: 5
Views: 3,218
Posted By myrna
tview

The tview alignment viewer is very simplistic but I have found it better than maqview (it comes as part of samtools). You can convert a maq alignment to a binary SAM file using the maq2sam-long...
Forum: Bioinformatics 02-15-2009, 08:36 AM
Replies: 236
Views: 569,720
Posted By myrna
Suboptimal hits

Novoalign will do this for you. You might have to play around with the parameters to get exactly what you want (how many suboptimal hits, how suboptimal etc).

Ryan
Forum: Bioinformatics 01-22-2009, 07:20 AM
Replies: 28
Views: 14,427
Posted By myrna
miRNA alignment

I use a very similar approach, but I first collapse identical reads before aligning (to avoid aligning the same let-7 and other abundant miRNA reads hundreds of thousands of times. You can then...
Forum: Bioinformatics 01-20-2009, 09:57 PM
Replies: 292
Views: 151,929
Posted By myrna
indelpe vs samtools indels

Hi Heng Li.
Could you comment on how the indel detection works in SAM pileups vs MAQ indelpe? I am seeing many more indels in my SAM pileup generated from a MAQ alignment (as compared to the output...
Forum: Bioinformatics 12-29-2008, 09:49 AM
Replies: 8
Views: 3,912
Posted By myrna
I'm glad to see that someone out there is seeing...

I'm glad to see that someone out there is seeing the same issue. I have isolated the problem and made a simple workaround. The converter is expecting certain fields in the export file to be filled,...
Forum: Bioinformatics 12-16-2008, 10:26 AM
Replies: 23
Views: 7,743
Posted By myrna
I'm glad you brought this up dvh. Perhaps a...

I'm glad you brought this up dvh. Perhaps a naive question, but isn't it possible to run 16 (unthreaded) instances of novoalign on your 16-core server and see similar performance?

Cheers,
...
Forum: Bioinformatics 12-16-2008, 06:46 AM
Replies: 23
Views: 7,743
Posted By myrna
I just wanted to note that Novoalign is free for...

I just wanted to note that Novoalign is free for academic use and the main difference between the free and paid version is that the latter supports threading. The free version should be fine for...
Forum: Bioinformatics 12-15-2008, 02:49 PM
Replies: 23
Views: 7,743
Posted By myrna
I see. I have tried it for human miRNA libraries...

I see. I have tried it for human miRNA libraries and it is quite slow (especially if you don't have access to a cluster). I would strongly advise using Novoalign for miRNAs instead of SOAP, but I...
Forum: Bioinformatics 12-15-2008, 02:42 PM
Replies: 23
Views: 7,743
Posted By myrna
How long does SOAP take (on average) to align a...

How long does SOAP take (on average) to align a single lane of data on a single CPU?

Thanks,

Ryan
Forum: Bioinformatics 11-19-2008, 10:55 AM
Replies: 513
Views: 199,929
Posted By myrna
Bowtie on a Mac

I found a way to fix the memory issue I mentioned in this thread on a Mac. It seems that the binary was run as a 32-bit intel process, which forces it to use 32-bit memory addressing. This meant...
Forum: Bioinformatics 11-18-2008, 01:57 PM
Replies: 513
Views: 199,929
Posted By myrna
memory issues when creating index file

Hi Ben.
Thanks for your prompt reply. This time around I see this error (after quite awhile):

bowtie-build-packed(14780) malloc: *** mmap(size=2860744704) failed (error code=12)
*** error:...
Forum: Bioinformatics 11-18-2008, 08:57 AM
Replies: 513
Views: 199,929
Posted By myrna
memory issues when creating index file

I am unable to index the human genome on my MacPro (16G RAM). I have the same problem when using the provided Mac binary or compling from source. I have posted the error output below.

Any ideas?...
Forum: Illumina/Solexa 11-10-2008, 08:16 AM
Replies: 8
Views: 3,879
Posted By myrna
Bowtie for miRNA alignment

How does Bowtie handle read trimming for miRNA data? Does it recognize the adaptor in advance and only align the pre-adaptor portion of the read? Or does it do a local alignment of the full read...
Forum: Illumina/Solexa 11-09-2008, 08:36 PM
Replies: 8
Views: 3,879
Posted By myrna
3' extensions

Hi Leo.
From what is known about miRNA target selection, the 3' extensions should not affect the interaction between a miRNA and its target. If you take this perspective, then the sum of all tags...
Forum: Illumina/Solexa 11-09-2008, 12:51 PM
Replies: 8
Views: 3,879
Posted By myrna
untemplated 3' additions

The 3' variability of miRNAs is a headache for both mapping and quantitation. We have recently adopted Novoalign for mapping miRNA-seq reads, since it allows multiple mismatches while still finding...
Forum: Bioinformatics 10-20-2008, 02:48 PM
Replies: 236
Views: 569,720
Posted By myrna
Bowtie

Hi Jerry.
How well (if at all) are indels handled by Bowtie? I have found Novoalign to handle gaps better than Maq and SOAP. By the way, I am looking forward to seeing the release of TopHat....
Forum: Bioinformatics 09-28-2008, 12:24 PM
Replies: 5
Views: 3,218
Posted By myrna
maqview

Why not just use maqview?

http://maq.sourceforge.net/maqview.shtml
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