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Forum: Genomic Resequencing 04-29-2015, 06:42 AM
Replies: 0
Views: 1,931
Posted By Nick
SOAPindel with bwa-mem

Has anyone run SOAPindel on sequences aligned with bwa-mem? It seems to have trouble interpreting some of the lines of the bam.
Forum: Bioinformatics 02-12-2015, 06:36 AM
Replies: 3
Views: 1,751
Posted By Nick
The version was 0.2.5a4, May 2 2014. We tried...

The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.
Forum: Bioinformatics 02-11-2015, 05:30 AM
Replies: 3
Views: 1,751
Posted By Nick
Pindel memory usage 30x whole genome

How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says it is processing a window with only 1000 reads.
Forum: Bioinformatics 09-12-2014, 07:57 AM
Replies: 0
Views: 777
Posted By Nick
CHIApet tools mapping output question

I'm trying to figure out the ouput .map files from chiapet tools mapper step. It generated a foo.linker_b.1.link.map, foo.linker_b.2.link.map, and foo.linker_b.c.link.map (along with...
Forum: RNA Sequencing 02-19-2014, 04:14 PM
Replies: 5
Views: 3,186
Posted By Nick
I'm looking at this SRA entry ...

I'm looking at this SRA entry
http://www.ncbi.nlm.nih.gov/sra?term=SRX142112
Forum: RNA Sequencing 02-19-2014, 11:34 AM
Replies: 5
Views: 3,186
Posted By Nick
Paired end RNA-seq orientation

Can someone explain to me what the orientation in paired-end RNA-seq data means? Is forward/forward the standard orientation? How does this affect tophat options, just specify unstranded Rna-seq?
Forum: Bioinformatics 09-19-2013, 07:59 AM
Replies: 23
Views: 31,003
Posted By Nick
This finally worked for me. The home mounted via...

This finally worked for me. The home mounted via NFS was not an issue. I also discovered that trying to change the default ncbi directory caused a lot issues, as a ~/ncbi directory was created...
Forum: Bioinformatics 03-15-2012, 08:18 AM
Replies: 1
Views: 1,700
Posted By Nick
Wig Bed Overlap

Hi All,
I want to trim my wig file to contain only regions that are overlapping features in a bed file. Anyone know a way to do this? Trying not to code up something when it seems like it should...
Forum: Bioinformatics 01-27-2012, 11:27 AM
Replies: 514
Views: 218,228
Posted By Nick
I know this thread is quite old, but just wanted...

I know this thread is quite old, but just wanted to point out this is not normal.
http://sourceforge.net/tracker/index.php?func=detail&aid=3049179&group_id=236897&atid=1101606
The search tree is...
Forum: Bioinformatics 07-12-2011, 07:36 AM
Replies: 5
Views: 8,658
Posted By Nick
allbowtie2sam.pl

I came across this thread with the same issue. As you said bowtie2sam.pl only takes the best read. That is much harder to do than just converting all the hits. I edited the file to print all the...
Forum: General 06-22-2011, 07:19 AM
Replies: 0
Views: 1,949
Posted By Nick
Unpaired reads in paired data

I have a paired read dataset in sam format. However some of the reads are unpaired with #0 a the end of their names. The flags indicate these are all optical duplicates. Why would I be missing the...
Forum: Bioinformatics 03-04-2011, 09:17 AM
Replies: 1
Views: 1,831
Posted By Nick
Bowtie: number of alignments

I'm using bowtie in repetitive regions and need all possible alignments of these reads. My question is about the backtracking mentioned in the original bowtie paper,...
Forum: Bioinformatics 09-02-2010, 09:09 AM
Replies: 2
Views: 1,898
Posted By Nick
SRF metadata

What information is in the SRF meta-data other than read lengths and pairing info? Broad question I know but does srf_info print it all out? Is the information in the trace name in a certain...
Forum: Bioinformatics 09-01-2010, 05:22 AM
Replies: 2
Views: 1,176
Posted By Nick
The .xsd's for files are here: ...

The .xsd's for files are here:
http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_2-0/

I was under the impression they have to be including with all submissions to SRA. I've ended up...
Forum: Bioinformatics 08-31-2010, 11:17 AM
Replies: 2
Views: 1,176
Posted By Nick
Standard XMLs for sequence

I'm trying to interpret XMLs I have that came with data from EGA. I'm told they are in the standard format for sequence data submitted to NCBI and EBI. Are there style sheets to display them in a...
Forum: Bioinformatics 06-30-2010, 12:07 PM
Replies: 0
Views: 1,949
Posted By Nick
Quality recalibration

I am working on using reads from regions that are not traditionally mapped(telomere), and am wondering about the GATK quality recalibration. As I understand it does so on an aligned BAM file. Are...
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