Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Error When Running Generate Pileup
0
gravatar for Alison Gardner
7.3 years ago by
Alison Gardner • 20
Alison Gardner • 20 wrote:
Hello, I am aligning Illumina paired end sequence using BWA, then run SAM-to- BAM resulting in a 1.1 Gb file. But when I then generate pileup on this file column 4 (consensus bases) are all N's and the file is now 8.4 Gb. Can someone tell me what might be going on? Any help much appreciated. Thanks Alison Gardner Neurogenetics Research Program, SA Pathology (at Women's and Children's Hospital), Level 9, Clarence Rieger Bldg., 72 King William Road, North Adelaide, S.A., Australia, 5006
bwa alignment • 823 views
ADD COMMENT • link •
modified 7.3 years ago by Nicola Nadeau • 40 • written 7.3 years ago by Alison Gardner • 20
0
gravatar for Nicola Nadeau
7.3 years ago by
Nicola Nadeau • 40
Nicola Nadeau • 40 wrote:
I would check what format your files were in to start with and that you had converted them sanger fastq before running BWA. I've had this problem before and it was because of the format which caused all the quality scores to be too low meaning all bases were called as Ns (I think they had already been converted to fastq sanger and I didn't realise and converted them again). Nicola
ADD COMMENT • link written 7.3 years ago by Nicola Nadeau • 40
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour