Question: How to avoid multiple mapped while no mismatch allow
0
gravatar for cv120345
4 weeks ago by
cv1203450
cv1203450 wrote:

I have read many manuals of alignment tools, many of them deal the multiple mapped by reporting the best alignment base on their alignment score (such as bowtie,BWA), but i want to know if i already set the mismatch as zero, then all multiple mapped should be same score right? What can i do to avoid reads that can find multiple perfectly matches?

rna-seq chip-seq alignment • 103 views
ADD COMMENTlink modified 4 weeks ago by dariober11k • written 4 weeks ago by cv1203450

but i want to know if i already set the mismatch as zero, then all multiple mapped should be same score right?

What do you mean exactly?

ADD REPLYlink written 29 days ago by h.mon30k

i can understand if mapping with allowing some mismatches there will be different in alignment score, but if i don't allow any mismatch it should be all perfectly match and same score.

ADD REPLYlink written 29 days ago by cv1203450
1
gravatar for dariober
4 weeks ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

What can i do to avoid reads that can find multiple perfectly matches

If by that you mean to filter out reads that map equally well to multiple locations, then you should filter by MAPQ score in the alignment file, e.g. samtools view -b -q 5 in.bam > out.bam. The exact MAPQ threshold you use for filtering shouldn't matter much since most reads usually have either very low or very high mapq.

Consider also that a read can have high MAPQ even with some mismatches so setting the number of mismatches to zero could be too stringent and it could introduce some biases since some mismatches may be genuine SNPs.

ADD COMMENTlink written 4 weeks ago by dariober11k

The purpose i want to have this kind of restriction owing to i trying to compare genes with similar sequence, i hope to avoid reads that is hard to distinguish from each other.

ADD REPLYlink written 29 days ago by cv1203450

Can you provide an example of alignments you want to keep and examples that you want to filter out?

ADD REPLYlink written 29 days ago by dariober11k
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