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Forum: Academic/Non-Profit Jobs 04-22-2017, 09:16 PM
Replies: 7
Views: 1,495
Posted By nilshomer
bigmw, having hired in more than a few software...

bigmw,
having hired in more than a few software developers (across all levels) into academia, I totally get where your coming from, including the challenges of hiring from and benefits of working in...
Forum: Academic/Non-Profit Jobs 04-22-2017, 02:28 PM
Replies: 7
Views: 1,495
Posted By nilshomer
To be honest, the compensation seems a bit low...

To be honest, the compensation seems a bit low compared to industry standards, even for only a few years of experience. Remember, your competing not only against developers in biotech, but also...
Forum: Bioinformatics 06-29-2013, 09:07 PM
Replies: 1
Views: 2,369
Posted By nilshomer
The mapall command requires you to specify the...

The mapall command requires you to specify the mapping algorithms, so something like:
tmap mapall -f reference.fas -r lib.fastq -s out.sam map1 map2 map3

See:...
Forum: Ion Torrent 06-29-2013, 09:02 PM
Replies: 9
Views: 5,486
Posted By nilshomer
BFAST and TMAP are not related, as the latter is...

BFAST and TMAP are not related, as the latter is derived from BWA and customized for Ion Torrent data, while the former was primarly used for SOLiD data alignment and the early days of Ion Torrent...
Forum: Bioinformatics 06-29-2013, 08:37 PM
Replies: 9
Views: 10,297
Posted By nilshomer
For those who may come to this thread through a...

For those who may come to this thread through a web search:
http://sourceforge.net/apps/mediawiki/picard/index.php?title=Using_Snappy_in_Picard
Forum: Bioinformatics 06-29-2013, 08:32 PM
Replies: 63
Views: 28,352
Posted By nilshomer
There was no desire from the folks maintaining...

There was no desire from the folks maintaining samtools to take over the development and add it. Sorry for the delayed response.
Forum: Bioinformatics 10-11-2012, 05:56 PM
Replies: 4
Views: 619
Posted By nilshomer
The CS tag should give ALL the colors, not just...

The CS tag should give ALL the colors, not just the aligned portion.
Forum: Bioinformatics 10-09-2012, 04:21 PM
Replies: 4
Views: 619
Posted By nilshomer
Seems like time for a perl one liner. Try this: ...

Seems like time for a perl one liner. Try this:
cat <in.sam> | grep -v "^@" | perl -ne '$_ =~ s/\t.*CS:Z:([^\t]+).*/\n$1/g; print ">$_";'
Forum: Bioinformatics 10-09-2012, 04:06 PM
Replies: 2
Views: 1,136
Posted By nilshomer
The *csfasta files do not have any quality...

The *csfasta files do not have any quality information, you probably need to input the *qual files as well.
Forum: Bioinformatics 10-01-2012, 07:01 PM
Replies: 6
Views: 1,709
Posted By nilshomer
A few things, the "-t" option doesn't require an...

A few things, the "-t" option doesn't require an argument, and you have forgotten to create a base space version as well. See the bfast manual that comes with the distribution for examples (Chapter...
Forum: Bioinformatics 09-27-2012, 09:57 PM
Replies: 6
Views: 1,709
Posted By nilshomer
It looks like your index is corrupt, try...

It looks like your index is corrupt, try rebuilding your indexes.
Forum: Illumina/Solexa 09-26-2012, 09:53 AM
Replies: 1
Views: 665
Posted By nilshomer
They are IUPAC codes, and most likely...

They are IUPAC codes, and most likely heterozygous variants.
Forum: Bioinformatics 09-07-2012, 02:04 PM
Replies: 9
Views: 2,586
Posted By nilshomer
Try "make clean" then "make", but also read the...

Try "make clean" then "make", but also read the README. If you still get a seg fault, please post a test case to [email protected] The maintainer (me) is responsive.
Forum: Clinical Sequencing 08-29-2012, 10:12 AM
Replies: 1
Views: 4,404
Posted By nilshomer
CAP Clinical NGS Checklist

It looks like the check list is out for CAP clinical next-gen, though $729: http://www.bio-itworld.com/els/08/28/12/CAP-releases-clinical-NGS-checklist.html
Forum: Clinical Sequencing 08-27-2012, 03:46 PM
Replies: 29
Views: 11,186
Posted By nilshomer
Who is doing clinical sequencing here?

Hello all, it would be fun to see who at seqanswers.com is doing clinical sequencing. Perhaps we can also compile a list of companies offering ClinSeq or Clinomics, with possibly entries in the...
Forum: Bioinformatics 08-27-2012, 03:43 PM
Replies: 2
Views: 1,121
Posted By nilshomer
BAM files are compacted and compressed, so you...

BAM files are compacted and compressed, so you wont be able to read them in a text viewer. Try converting back from BAM to SAM to see if you get the original SAM file.
Forum: Bioinformatics 08-19-2012, 10:53 AM
Replies: 9
Views: 2,586
Posted By nilshomer
Most likely you need to create a symbolic link to...

Most likely you need to create a symbolic link to the samtools source code, but you could post your error message or more info.
Forum: Bioinformatics 08-18-2012, 04:54 PM
Replies: 10
Views: 2,255
Posted By nilshomer
Please try inputting it exactly as you would in a...

Please try inputting it exactly as you would in a normal SAM file. The string will be written exactly as it is given. So you should include the tab characters as well. Here's what the manual says:...
Forum: Bioinformatics 08-18-2012, 01:39 PM
Replies: 27
Views: 7,945
Posted By nilshomer
It looks like your FASTA index is broken. Can...

It looks like your FASTA index is broken. Can you try rebuilding?


I am sorry, please try reducing your read set or the like to a manageable test case. Otherwise, I charge $5KUSD/hour ;)
Forum: Bioinformatics 08-18-2012, 01:29 PM
Replies: 9
Views: 2,586
Posted By nilshomer
Please post your answer so that others can...

Please post your answer so that others can benefit in the future.
Forum: Bioinformatics 08-18-2012, 01:28 PM
Replies: 10
Views: 2,255
Posted By nilshomer
It should work, but the only way to know is to...

It should work, but the only way to know is to try.
Forum: Bioinformatics 08-16-2012, 07:53 AM
Replies: 27
Views: 7,945
Posted By nilshomer
Could you post the full error message?

Could you post the full error message?
Forum: Personalized Genomics 08-15-2012, 02:40 PM
Replies: 9
Views: 4,650
Posted By nilshomer
The password is in the details/comment section of...

The password is in the details/comment section of the torrent file.
Forum: Core Facilities 08-13-2012, 08:00 PM
Replies: 4
Views: 2,610
Posted By nilshomer
Here's a site that I have not used that can help...

Here's a site that I have not used that can help facilitate selling extra capacity: http://blueseq.com/
Forum: Site Feedback/Suggestions 08-13-2012, 07:57 PM
Replies: 11
Views: 3,579
Posted By nilshomer
I am with you on this. I have it "remember me"...

I am with you on this. I have it "remember me" so that I am logged in, or I log in first thing. I then click "new posts" at the top page. I then open a new tab for each page I have not visited...
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