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Forum: Bioinformatics 10-12-2011, 04:09 AM
Replies: 0
Views: 1,166
Posted By mapper
Mapping to reference with IUB codes

Hi All,

Is there any software which can map reads to IUB coded reference for SOLiD data? The reason I am looking for this tools is..we have a data from SOLiD which is similar to bisulfite treated...
Forum: Bioinformatics 07-21-2011, 11:01 PM
Replies: 4
Views: 1,575
Posted By mapper
yes there are diff templates for diff workflows....

yes there are diff templates for diff workflows. You dont need cmap file for all applications. cmap file is required when you want to run pipeline like indel finding/ CNV analysis...

There are few...
Forum: Bioinformatics 07-19-2011, 07:22 PM
Replies: 4
Views: 1,575
Posted By mapper
If you use bioscope GUI for analysis .ini file...

If you use bioscope GUI for analysis .ini file will be generated automatically but if you want to run bioscope from command line , you need to create a ini file. ini is simple text file, you can use...
Forum: RNA Sequencing 03-15-2011, 09:18 AM
Replies: 5
Views: 3,147
Posted By mapper
check this link ...

check this link

ftp://ftp.ensemblgenomes.org/pub/plants/release-8/gtf/zea_mays/
Forum: Bioinformatics 03-02-2011, 08:58 PM
Replies: 8
Views: 5,054
Posted By mapper
Try running samtools tview command and see if you...

Try running samtools tview command and see if you are able to view alignments...If you can see alignments then there is nothing wrong with your bam files....

I have seen this kind of prob...
Forum: Bioinformatics 02-25-2011, 12:14 AM
Replies: 4
Views: 1,946
Posted By mapper
Hi Here are some links which will be helpful...

Hi

Here are some links which will be helpful


http://blog.bioteam.net/wp-content/uploads/2010/03/cdag-xgen-storageForNGS_v3.pdf
...
Forum: Bioinformatics 02-23-2011, 07:20 AM
Replies: 12
Views: 7,561
Posted By mapper
I believe it keeps one read per start position...

I believe it keeps one read per start position and discards other reads. I have seen these kind of alignments IGV...
Forum: Bioinformatics 02-22-2011, 10:24 PM
Replies: 12
Views: 7,561
Posted By mapper
I am not sure what "collapse all PCR reads...

I am not sure what "collapse all PCR reads mean"...Can you explain in more detail...

Picard mark reads as duplicates and remove it only when REMOVE_DUPLICATES is set to 'YES'...If you keep this...
Forum: Bioinformatics 02-22-2011, 10:06 PM
Replies: 16
Views: 8,407
Posted By mapper
Well, installing ROCKS cluster is as easy as...

Well, installing ROCKS cluster is as easy as installing OS on stand alone machine(I guess 10% more efforts are required)...doing configuration and setting up takes few hrs (2-3) when you do it for...
Forum: Bioinformatics 02-21-2011, 11:38 PM
Replies: 1
Views: 2,802
Posted By mapper
you can download SOLiD small RNA test dataset...

you can download SOLiD small RNA test dataset from this site.

http://solidsoftwaretools.com/gf/
Forum: Bioinformatics 02-21-2011, 11:36 PM
Replies: 12
Views: 7,561
Posted By mapper
you can use picard tools to remove PCR...

you can use picard tools to remove PCR duplicates...
Forum: Bioinformatics 02-21-2011, 11:30 PM
Replies: 16
Views: 8,407
Posted By mapper
we are using rocks from long time and its working...

we are using rocks from long time and its working fine....
Forum: Bioinformatics 02-16-2011, 01:36 AM
Replies: 5
Views: 1,720
Posted By mapper
I have also seen very large peaks with MACS...

I have also seen very large peaks with MACS ...you can either use peak splitter program...or you can try sissr which will give very sharp peaks....
Forum: Bioinformatics 01-05-2011, 02:11 AM
Replies: 0
Views: 1,383
Posted By mapper
Bowtie mapping with more mismatches

We have 50bp reads and want to map with bowtie with 6mm. However it seems that only 3 mm are allowed at max. I have tried to look on net and many people suggested to use -e option..I am not sure what...
Forum: Bioinformatics 11-29-2010, 03:29 AM
Replies: 1
Views: 3,534
Posted By mapper
bowtie mapping stats

How to print bowtie stats in a file??

I want to print this output( bowtie mapping stats) in a file...

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Forum: Bioinformatics 11-22-2010, 10:44 PM
Replies: 2
Views: 2,582
Posted By mapper
thnx ........

thnx ........
Forum: Bioinformatics 11-22-2010, 08:49 PM
Replies: 2
Views: 2,582
Posted By mapper
Uniquely mapped reads with bowtie

Hi all

Is there anyway to report only mapped tags in bowtie sam output?

I tried to map reads with bowtie with -m 1 --best and --strata parameter but in mapping output(sam) reads which are not...
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