Question: Error When Running Generate Pileup
gravatar for Alison Gardner
7.3 years ago by
Alison Gardner20 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 COMMENTlink modified 7.3 years ago by Nicola Nadeau40 • written 7.3 years ago by Alison Gardner20
gravatar for Nicola Nadeau
7.3 years ago by
Nicola Nadeau40 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 COMMENTlink written 7.3 years ago by Nicola Nadeau40
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