SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 8 of 8
Search took 0.00 seconds.
Search: Posts Made By: craczy
Forum: Bioinformatics 08-20-2015, 02:17 PM
Replies: 36
Views: 5,511
Posted By craczy
In an attempt to make it easier to use Isaac2, we...

In an attempt to make it easier to use Isaac2, we will make the packed index reference for commonly used genomes on BaseSpace. At the moment, the only 2 genomes available are hg19 and mm9. Feel free...
Forum: Bioinformatics 07-28-2015, 12:18 PM
Replies: 36
Views: 5,511
Posted By craczy
My mistake. Apologies. It is not the...

My mistake. Apologies. It is not the sorted-reference.xml but the tarball created by 'isaac-pack-reference':

rm -rf Temp
isaac-unpack-reference -j 1 -w 6 -i packed-reference.tar.gz
Forum: Bioinformatics 07-28-2015, 06:07 AM
Replies: 36
Views: 5,511
Posted By craczy
The input file should be the...

The input file should be the 'sorted-reverence.xml', not the current directory:

This should work:

isaac-unpack-reference -j 1 -w 6 -i sorted-reference.xml

Remember to remove the already...
Forum: Bioinformatics 07-24-2015, 09:02 AM
Replies: 36
Views: 5,511
Posted By craczy
This looks correct, but surprising. Did you...

This looks correct, but surprising. Did you specify something like "-w 1" on the command line by any chance?

All the kmers are indexed in on single data file (kmer-positions-32-0.dat), which is...
Forum: Bioinformatics 07-22-2015, 12:12 PM
Replies: 36
Views: 5,511
Posted By craczy
Unfortunately it has. The index contains extra...

Unfortunately it has. The index contains extra information about the reference and with isaac2 that information has changed. Specifically, in the isaac2 index we are keeping track for each position...
Forum: Bioinformatics 07-22-2015, 10:06 AM
Replies: 36
Views: 5,511
Posted By craczy
First of all sorry for the confusion around the...

First of all sorry for the confusion around the meaning of the "-j" option across the different tools, and about the inconvenience that you experienced. To clarify:

- isaac-align: this is a single...
Forum: Bioinformatics 07-15-2013, 01:51 AM
Replies: 23
Views: 5,972
Posted By craczy
Hi GenoMax, if you managed to run it under...

Hi GenoMax,

if you managed to run it under HAS, why don't you use the command line generated by HAS? That command line can be found either on the standard output, or at the beginning of the log...
Forum: Bioinformatics 06-24-2013, 12:21 AM
Replies: 23
Views: 5,972
Posted By craczy
Hi oiiio You would need a lot more than 12GB...

Hi oiiio

You would need a lot more than 12GB memory. Try "-m 48" instead.

Thanks,

Come
Showing results 1 to 8 of 8

 


All times are GMT -8. The time now is 01:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO