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Forum: Bioinformatics 02-02-2010, 08:34 AM
Replies: 2
Views: 1,181
Posted By anusha
Analysing the Bowtie output.

Hi all,

I am right now working with bowtie..trying to map the RNA seq.
I got the SAM output and now i want to see the mapping occuring on the genome. Is there any tool which does the annotation...
Forum: Bioinformatics 01-21-2010, 07:52 AM
Replies: 4
Views: 2,905
Posted By anusha
Trimming or filtering the data from Solid

Hi ..

I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest....
Forum: SOLiD 01-21-2010, 06:24 AM
Replies: 1
Views: 1,925
Posted By anusha
Trimming or filtering the data from Solid

Hi ..

I have got the solid csfatsa file and the data has lot of dots in the sample. So i there any way i can trim or filter the Data in Bowtie,Maq or in another tools that you could suggest....
Forum: Bioinformatics 01-20-2010, 11:14 AM
Replies: 7
Views: 2,500
Posted By anusha
Hi I tried and able to run in Bowtie but it shows...

Hi I tried and able to run in Bowtie but it shows a very low alignment. so i am trying to do comparison using maq. while i am running maq i got the following error message.

[anusha@njmscluster...
Forum: Bioinformatics 01-19-2010, 11:24 AM
Replies: 7
Views: 2,500
Posted By anusha
Thank you.I tried in galaxy but i am getting the...

Thank you.I tried in galaxy but i am getting the output file as fastaqsanger.
I am now checking out whether i can use that in bowtie. If this doesnt work i wil try in BFAST's.
Forum: Bioinformatics 01-19-2010, 06:51 AM
Replies: 7
Views: 2,500
Posted By anusha
Bowtie -Color spaces

Hi i trying to work with bowtie on color spaces.
I got the csfasta and qual files from the SOLID and now need to run bowtie to analyse it. But bowtie reads the fastaq files.
Can anyone help me in...
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