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Search: Posts Made By: Ka123$
Forum: General 04-25-2010, 06:47 PM
Replies: 13
Views: 9,037
Posted By Ka123$
THanks so much, I will take a look at deepbase...

THanks so much,
I will take a look at deepbase and get back to you soon.
Forum: General 04-20-2010, 11:21 AM
Replies: 13
Views: 9,037
Posted By Ka123$
Can anyone suggest more info in looking into...

Can anyone suggest more info in looking into piRNA mappers and analysis?
Forum: Bioinformatics 10-09-2009, 10:45 AM
Replies: 236
Views: 596,744
Posted By Ka123$
Hi apfejes, I had sent you my email ID earlier...

Hi apfejes,
I had sent you my email ID earlier last week. I was wondering if you got it or not....Please can you check again. I am sending you a email with this thread and you can reply to me on...
Forum: Bioinformatics 09-30-2009, 03:59 PM
Replies: 236
Views: 596,744
Posted By Ka123$
Thanks so much anthony ! If you could compile and...

Thanks so much anthony ! If you could compile and email me that will be great!!!! I appreciate it so much!.......
Forum: Bioinformatics 09-30-2009, 03:31 PM
Replies: 236
Views: 596,744
Posted By Ka123$
Hi Anthony, so here is what I am doing. We have...

Hi Anthony,
so here is what I am doing. We have decided to stick with the GERALD files to convert it to wig.......(PI's order !)
I checked for unaligned files and none were there.
I have a .export...
Forum: Bioinformatics 09-30-2009, 02:08 PM
Replies: 236
Views: 596,744
Posted By Ka123$
can anyone let me know why findpeaks...

can anyone let me know why findpeaks separatereads.jar command cannot create a log file when I use the GERALD aligned files or the bowtie aligned files?
In GERALD aligned files I indicated elandext...
Forum: Bioinformatics 09-28-2009, 06:49 PM
Replies: 236
Views: 596,744
Posted By Ka123$
First of, thanks so much for all your guidance,...

First of, thanks so much for all your guidance, from both of you!
I really appreciate it so much!

I previously tried using bowtie aligner. As bowtie aligner gave me only one separatefile.gz and I...
Forum: Bioinformatics 09-28-2009, 10:33 AM
Replies: 236
Views: 596,744
Posted By Ka123$
Thanks to both kmcarr and apfejes ! I did...

Thanks to both kmcarr and apfejes !
I did belive that GERALD generates the Eland format files. But when I used GERALD files to perform a separate reads according to findpeaks and I used ELAND as an...
Forum: Bioinformatics 09-28-2009, 03:10 AM
Replies: 236
Views: 596,744
Posted By Ka123$
If I would directly perform separate reads and...

If I would directly perform separate reads and sort reads on the GERALD alignment files what type of aligner do I need to specify? GERALD/Eland if specified give me an error on fndpeaks
Error: ...
Forum: Bioinformatics 09-28-2009, 02:35 AM
Replies: 236
Views: 596,744
Posted By Ka123$
what kind of formats are BUSTARD and GERALD files...

what kind of formats are BUSTARD and GERALD files from solexa?
Forum: Bioinformatics 09-24-2009, 09:27 AM
Replies: 236
Views: 596,744
Posted By Ka123$
Thanks a lot I will try all the options you gave...

Thanks a lot I will try all the options you gave me and let u know how it worked for me.
Forum: Bioinformatics 09-24-2009, 08:57 AM
Replies: 236
Views: 596,744
Posted By Ka123$
sortpeaks

Yeah sure,
I had this huge I human seq reads that I aligned using bowtie. This bowtie alignment I need to convert into wig files. So I have been using the separateReads as the first step in...
Forum: Genomic Resequencing 09-24-2009, 07:28 AM
Replies: 9
Views: 4,921
Posted By Ka123$
If I used the SeparateReads from findpeaks...

If I used the SeparateReads from findpeaks directly on GERALD.export files ,specifying the -aligner eland, I get an error message: Any help?
Version: Initializing class SeparateReads ...
Forum: Bioinformatics 09-24-2009, 06:51 AM
Replies: 236
Views: 596,744
Posted By Ka123$
Solexa findpeaks

Using Findpeaks sort reads on bowtie mapped alignment is taking up too much memory......!!!!! So I am trying using the GERALD maps reads directly from solexa to convert to wig files...I believe the...
Forum: Genomic Resequencing 09-07-2009, 02:58 PM
Replies: 9
Views: 4,921
Posted By Ka123$
Sort files

Ohk I got to work the sort files on my separate files to run! But it went out of memory!!!
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
Any suggestion on how...
Forum: Genomic Resequencing 09-07-2009, 02:00 PM
Replies: 9
Views: 4,921
Posted By Ka123$
sortFiles problem

Hi , Can anyone help me with this problem please.
I have bowtie aligned seq and trying to convert it into wigfiles using the findpeak.
so I performed a SeparateReads and saved it in a folder as...
Forum: Bioinformatics 07-30-2009, 07:15 PM
Replies: 11
Views: 4,703
Posted By Ka123$
Hi Fejes, According to your previous blog help ...

Hi Fejes,
According to your previous blog help
"With the latest version (4.0.x), the convertToBed.jar application should be invoked as:

"java -jar /path/to/ConvertToBed.jar -input GaP_align...
Forum: Bioinformatics 07-21-2009, 08:27 AM
Replies: 57
Views: 39,995
Posted By Ka123$
Boetietobed

Thanks so much Mr.Anthony,
I appreciate your help a lot!
I am a molecular biologist trying out some basic programming . SO thanks to you and everyone else on the forum for the patience and all...
Forum: Bioinformatics 07-21-2009, 03:28 AM
Replies: 57
Views: 39,995
Posted By Ka123$
apfejes thanks for the reply, This might be a...

apfejes thanks for the reply,
This might be a very basic problem at the command line as it says command not found....
I am a unix dummy and am playing with this.....
I want to use the convert...
Forum: Bioinformatics 07-20-2009, 06:13 PM
Replies: 57
Views: 39,995
Posted By Ka123$
Is there a way to convert bowtie aligned files to...

Is there a way to convert bowtie aligned files to a BED files in unix?
I tried following the directions on the http://vancouvershortr.wiki.sourceforge.net/BowtieToBedFormat. But I get a error...
Forum: Bioinformatics 07-20-2009, 03:24 AM
Replies: 11
Views: 4,703
Posted By Ka123$
hello all

When I try coverting my bowtie to BED file using bowtie converter on http://vancouvershortr.wiki.sourceforge.net/ConvertToBed
and execute it I get a message : could not locate a bowtie index...
Forum: Bioinformatics 07-17-2009, 06:16 PM
Replies: 11
Views: 4,703
Posted By Ka123$
File format of bowtie

Hi ,
Does anyone know what file format does the bowtie output give after aligning the solexa data to a reference.Do we need to convert this to a BED file to be able to analyse in cisGenome? or can...
Forum: Bioinformatics 07-16-2009, 04:50 PM
Replies: 57
Views: 39,995
Posted By Ka123$
HI Brent, My email is com_bio@yahoo.com.Thanks ...

HI Brent,
My email is com_bio@yahoo.com.Thanks
What kind of format are (GERALD) aligned output files?Aligned files are mapped files I suppose......just two terminologies.....?
Forum: Bioinformatics 07-16-2009, 04:48 PM
Replies: 57
Views: 39,995
Posted By Ka123$
Bowtie to Bed files

Hi Brent
could you also help me with the perl script to convert bowtie to BED? I am not a perl person. Also can find peak convert the bowtie-align files to a cisGenome compatible file?
THanks
Ka
Forum: Bioinformatics 07-16-2009, 11:53 AM
Replies: 11
Views: 4,703
Posted By Ka123$
Thanks Ben

after align do we do map on a different software?
I thought bowtie can do the mapping too.....
Have u come across a segmentation error when u run maptool?

again thanks for your input!
Showing results 1 to 25 of 27

 


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