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Search: Posts Made By: 12jrowley2
Forum: Bioinformatics 06-08-2013, 06:00 PM
Replies: 3
Views: 2,778
Posted By 12jrowley2
samtools mpileup truncated output

Has this been resolved, I am having the same problem with no asterisks after 0 with multiple sample mpileup
Forum: Bioinformatics 08-09-2011, 12:05 PM
Replies: 6
Views: 2,409
Posted By 12jrowley2
Thanks for your input. Samtools pipes output...

Thanks for your input. Samtools pipes output line by line- as they are processed- into BCF-tools, thus the benefit of piping, right? I tried the -b option as troubleshooting to figure out why -v...
Forum: Bioinformatics 08-09-2011, 10:59 AM
Replies: 6
Views: 2,409
Posted By 12jrowley2
samtools doesn't read whole data

I updated to samtools 0.1.17 from 0.1.12a. Now samtools doesn't seem to begin processing the data:

./samtools-0.1.17/samtools mpileup -I -C 0 -Q 40 -u -f ./hg19.fasta...
Forum: Bioinformatics 08-09-2011, 10:11 AM
Replies: 1
Views: 2,448
Posted By 12jrowley2
running samtools mpileup with nohup -redirect STDERR?

I have seen multiple people getting this error - when piping mpileup into bcftoos -
[bcf_sync] incorrect number of fields (0 != 5). Corrupted file?
I was getting this error until I saw this...
Forum: Bioinformatics 08-08-2011, 11:55 AM
Replies: 6
Views: 2,409
Posted By 12jrowley2
Did this get resolved? I am having the same...

Did this get resolved? I am having the same issue.
Jesse
Forum: RNA Sequencing 05-27-2011, 01:38 PM
Replies: 2
Views: 2,450
Posted By 12jrowley2
setting parameters for Novoalign 2-6 bp insertions deletions

I am looking for insertions 2-6 bp in length in the native novoalign output - but see that novoalign did not output any insertions greater than 1 bp. Am I looking for this wrong?

awk '$14 ~...
Forum: Bioinformatics 04-07-2011, 09:35 AM
Replies: 4
Views: 3,629
Posted By 12jrowley2
TopHat mapping outside reference contig

I also received this error
Mate Alignment start must be <= reference sequence length on reference
when trying to run picard to convert to BAM
was this ever resolved?
thanks,
Forum: RNA Sequencing 04-06-2011, 03:01 PM
Replies: 8
Views: 2,971
Posted By 12jrowley2
Bam header formatting from bowtie incompatible with IGB

I do index the bam files.
I think you're right about the header being wrong, but using -bhS in this case does not solve the issue, because the @SQ lines are absent.

I tried adding the header as...
Forum: RNA Sequencing 04-06-2011, 11:18 AM
Replies: 8
Views: 2,971
Posted By 12jrowley2
Bam Error in IGB

Yeah I also got the same error - processed my bowtie reads the same way. Any hints yet?
Forum: Bioinformatics 02-16-2011, 09:32 AM
Replies: 5
Views: 3,430
Posted By 12jrowley2
MISO - got it thanks

Thanks, I got it working now.
Forum: Bioinformatics 02-15-2011, 10:53 PM
Replies: 5
Views: 3,430
Posted By 12jrowley2
Miso

good to hear it is working for you - did you run it using the TandemUTR or A3SS/A5SS indexes? for the input file I navigate to the...
Forum: Bioinformatics 02-15-2011, 02:51 PM
Replies: 5
Views: 3,430
Posted By 12jrowley2
Anyone Tried MISO with Posted GFF files?

I am trying out the Burge lab's MISO program for isoform analysis. I want to use the mm9 file posted on their website, but within the mm9 folder are many subfolders with different pickled GFF...
Forum: RNA Sequencing 12-03-2010, 10:41 AM
Replies: 2
Views: 2,406
Posted By 12jrowley2
multiple sample differential RNA editing/SNP after novoalignment

Any programs out there that will take multiple aligned RNA-seq datasets from treatment and control samples with biological replicates and compare them for differences in single base pair...
Forum: Introductions 12-03-2010, 10:26 AM
Replies: 0
Views: 1,031
Posted By 12jrowley2
Hello

Hi everyone, I'm a post-doc at the University of Utah. I've been working on some transcriptome analysis using paired GAII seq reads in platelets. The posts I've seen here have been very helpful. ...
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