SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.01 seconds.
Search: Posts Made By: plichel
Forum: Bioinformatics 05-30-2011, 06:16 AM
Replies: 20
Views: 5,054
Posted By plichel
Not entirely sure, but I think for cnv detection...

Not entirely sure, but I think for cnv detection this software is not suited.
Forum: Bioinformatics 05-26-2011, 11:43 AM
Replies: 29
Views: 12,556
Posted By plichel
I guess it will greatly depend on coverage and...

I guess it will greatly depend on coverage and uniqueness of the alignment.
Suppose you have 30x and see indeed at a particular position 30 ore more softclipped reads supporting the breakpoint and...
Forum: Bioinformatics 05-26-2011, 02:21 AM
Replies: 20
Views: 5,054
Posted By plichel
Then you are pobably done with building/compiling...

Then you are pobably done with building/compiling variationHunter.

After I builded the project I can find these binaries:
calProbMinEditRead
convertToInvLRProbMinEditDist
sortString...
Forum: Bioinformatics 05-25-2011, 04:12 AM
Replies: 20
Views: 5,054
Posted By plichel
you are trying to execute the makefile as a...

you are trying to execute the makefile as a shellscript. this doesnt work. you have run it using make. to build the (any) project using make, you usually do simply:

make

make will automatically...
Forum: Bioinformatics 05-19-2011, 10:07 AM
Replies: 20
Views: 5,054
Posted By plichel
non human reference

could you advice how to run variation hunter with arbitrary reference genome. I have the impression that it assumes a certain hg assembly.
When running with the output of mrfast I get files like...
Forum: Bioinformatics 05-19-2011, 12:42 AM
Replies: 29
Views: 12,556
Posted By plichel
breakpoints

Does hydra also utilize partially mapped reads ?
I see a lot of softclipped alignments in my bwa aligned sam file. I am wondering whether this information is used when searching for breakpoints.
...
Forum: General 10-04-2010, 07:08 AM
Replies: 30
Views: 13,747
Posted By plichel
To not to waste threads, does anybody know...

To not to waste threads, does anybody know whether there is a read simulater that can sample also some known snps from, say, a dbsnp file or similar ?
Thanks !
Forum: Bioinformatics 05-12-2010, 03:03 PM
Replies: 83
Views: 275,424
Posted By plichel
I am not very familiar with all the...

I am not very familiar with all the biotechnology, so want to ask:
Is it possible to resolve which pair of reads come from the one, unique molecule ? (For instance, that the sequencer tracks this...
Forum: Bioinformatics 03-22-2010, 04:05 AM
Replies: 1
Views: 1,310
Posted By plichel
customize SAM/BAM format

Hi,

I want to analyse 454 data that cover exonic as well as intronic regions. Is it possible to hold this information in the bam and sam files ?
I could imagine to either (i) label each sequence...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 05:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO