I use Galaxy to analysis my chip-seq data and map reads by bowtie using default setting (In Galaxy leave "Bowtie settings to use" as defualt "most commonly used")
I found one of my reads:
@123
GGAAAATGATAAAAACCACACTGTAGAACATATTAG
+123
************************************
the mapping results is below:
123 16 chr6 103614979 255 36M * 0 0 CTAATATGTTCTACAGTGTGGTTTTTATCATTTTCC ************************************ XA:i:0 MD:Z:36 NM:i:0
as you see this read map to chr6 103614979
but I use blat to check the mapping quality (mm8/NCBI36): the blat outcome is below:
browser details YourSeq 36 1 36 36 100.0% 6 + 103614979 103615014 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98463554 98463589 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98467141 98467176 36
there are three perfect match which means this read is NOT unique match which can be fileterd. but bowtie give me no such information.
My question is commonly used option in Galaxy is so bad? or I miss some information?
I found one of my reads:
@123
GGAAAATGATAAAAACCACACTGTAGAACATATTAG
+123
************************************
the mapping results is below:
123 16 chr6 103614979 255 36M * 0 0 CTAATATGTTCTACAGTGTGGTTTTTATCATTTTCC ************************************ XA:i:0 MD:Z:36 NM:i:0
as you see this read map to chr6 103614979
but I use blat to check the mapping quality (mm8/NCBI36): the blat outcome is below:
browser details YourSeq 36 1 36 36 100.0% 6 + 103614979 103615014 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98463554 98463589 36
browser details YourSeq 36 1 36 36 100.0% 2 + 98467141 98467176 36
there are three perfect match which means this read is NOT unique match which can be fileterd. but bowtie give me no such information.
My question is commonly used option in Galaxy is so bad? or I miss some information?
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