SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: zack80.liu
Forum: RNA Sequencing 03-05-2011, 08:27 AM
Replies: 5
Views: 5,515
Posted By zack80.liu
Me too. I ran into the same problem... Any idea?

Me too. I ran into the same problem... Any idea?
Forum: Bioinformatics 03-02-2011, 02:45 PM
Replies: 3
Views: 3,211
Posted By zack80.liu
Isn't tophat also use bowtie to do the alignment?

Isn't tophat also use bowtie to do the alignment?
Forum: Bioinformatics 03-02-2011, 12:29 PM
Replies: 3
Views: 3,211
Posted By zack80.liu
Unhappy Paired-end reads mapped 50% while each pair reads mapped 80%

Hi all,

I am new to the RNA seq world. I have processed bunch of illumina paired end reads. The reported alignment is only 49%.. When I use bowtie to map each pair of the paired-end reads, I got...
Forum: Bioinformatics 03-01-2011, 09:08 AM
Replies: 6
Views: 4,952
Posted By zack80.liu
single read mapping can reach 80% # reads...

single read mapping can reach 80%

# reads processed: 34439174
# reads with at least one reported alignment: 27167675 (78.89%)
# reads that failed to align: 7271499 (21.11%)

Well paired...
Forum: Bioinformatics 03-01-2011, 06:43 AM
Replies: 6
Views: 4,952
Posted By zack80.liu
Plassaaw, I used mm9_with_junctions index...

Plassaaw,

I used mm9_with_junctions index which supposedly takes care of the exon-exon junctions .

When I run single reads on these two paired_end reads _1 and _2, 80% and 78% of the reads...
Forum: Bioinformatics 02-28-2011, 01:37 PM
Replies: 6
Views: 4,952
Posted By zack80.liu
This is a mouse cancer dataset. However not a lot...

This is a mouse cancer dataset. However not a lot indels are expected. Some of the samples are normal controls. Any more information needed?
Forum: Bioinformatics 02-28-2011, 10:15 AM
Replies: 6
Views: 4,952
Posted By zack80.liu
Percentage of mapped reads ?

Hi all,

I am new to the RNA seq world. I have processed bunch of illumina paired end reads. The reported alignment is only 49%.. I was wondering if this is normal. Here's the command and output....
Forum: Bioinformatics 02-10-2011, 09:50 AM
Replies: 3
Views: 1,483
Posted By zack80.liu
Thanks for the reply.

Thanks for the reply.
Forum: Bioinformatics 02-09-2011, 11:12 AM
Replies: 3
Views: 1,483
Posted By zack80.liu
What is this format? How to run bowtie on it.

I am a newbie to NGS. Please help.

I have the following file (I was told that it is a export file of illumina)

HWUSI-EAS1744 1 8 1 1165 18707 0 1 ...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 11:43 AM.


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