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Search: Posts Made By: shawn.mek
Forum: Industry Jobs! 03-12-2019, 06:37 AM
Replies: 0
Views: 1,868
Posted By shawn.mek
Looking for Global Bioinformatics Manager -CRISPR, siRNA, Cell line engineering, scre

For some reason, I can't post to Industry Jobs??

Maybe someone can move this there...

A great opportunity to work on cutting edge science with an amazing team!
...
Forum: Bioinformatics 05-18-2017, 06:40 AM
Replies: 8
Views: 2,717
Posted By shawn.mek
Actually, yes they did get the older version for...

Actually, yes they did get the older version for me and made it available temporarily. You can email them, and eventually, they will probably be able to put it somewhere for you to download. They...
Forum: Bioinformatics 10-31-2013, 01:32 PM
Replies: 9
Views: 3,355
Posted By shawn.mek
yeah, I'm torn on holding it in memory or not....

yeah, I'm torn on holding it in memory or not. Toy with different workflows
Forum: Bioinformatics 10-31-2013, 11:19 AM
Replies: 9
Views: 3,355
Posted By shawn.mek
I want to retrieve lots of regions efficiently,...

I want to retrieve lots of regions efficiently, but thanks for pointing me to faidx, I'll see how it works.
Forum: Bioinformatics 10-30-2013, 10:20 PM
Replies: 9
Views: 3,355
Posted By shawn.mek
The bowtie-inspect thing does get all the info...

The bowtie-inspect thing does get all the info out, but thats 3gb of info since I can't select a location
Forum: Bioinformatics 10-28-2013, 07:33 AM
Replies: 9
Views: 3,355
Posted By shawn.mek
Just to clarify, I mean using the index - giving...

Just to clarify, I mean using the index - giving it a chromosome name (fasta header) and location numbers, and getting back a sequence.

I don't want to run an alignment, just pull out the...
Forum: Bioinformatics 10-28-2013, 06:28 AM
Replies: 9
Views: 3,355
Posted By shawn.mek
Question Use Bowtie Index to get sequences using locations

We have the fasta files (obviously) for the hg19 genome, we used them to create a big Bowtie index.

I was hoping not to have to keep the fasta file. Instead just look up sequences in the Bowtie...
Forum: Bioinformatics 09-06-2013, 11:24 AM
Replies: 0
Views: 1,919
Posted By shawn.mek
Bowtie2 output fastq of paired reads where at least one in the pair aligns

Bowtie2 has the option on paired reads to spit out fastq files of things that fail to align concordantly (--un-conc <path>), and it has the option to spit out fastq files of things than align...
Forum: Bioinformatics 02-21-2013, 08:09 AM
Replies: 8
Views: 2,717
Posted By shawn.mek
Well, I am reproducing the analysis that used 56,...

Well, I am reproducing the analysis that used 56, but then doing additional analysis using 56 to go along with the old analysis.

If I use 57 to do the additional analysis I wouldn't have anything...
Forum: Bioinformatics 02-21-2013, 07:48 AM
Replies: 8
Views: 2,717
Posted By shawn.mek
Yeah, haven't heard back yet (it's been awhile),...

Yeah, haven't heard back yet (it's been awhile), but will post later if they ever tell me anything.

Any other possible workarounds you can think of?
Forum: Bioinformatics 02-21-2013, 07:25 AM
Replies: 8
Views: 2,717
Posted By shawn.mek
No I actually need 56, to match what was done...

No I actually need 56, to match what was done previously.

I'm not as concerned with up to date information, I am concerned with reproducing something.

I need those missing records, and I need...
Forum: Bioinformatics 02-21-2013, 07:04 AM
Replies: 8
Views: 2,717
Posted By shawn.mek
How do you download old RefSeq releases

If I need to run analysis using a specific release version of Refseq, is there a place to download it (say release 56)?

They are on release version 57 now, but I need my analysis to match someone...
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