I'm aligning WGS data from a HiSeq and getting very low percent mapping, like 30-35% of the input reads? The bam file of the same fastq reads shows > 99% mapping. I've tried pe mapping with --best and single read mapping leaving that off and using -e 10, but it didn't change much. These are long reads, 250 bp, and I indexed the hg19 using --ws 13.
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
Can
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From: Can Alkan calkan@users.sf.net
Sent: Wednesday, March 23, 2016 2:16 AM
To: [mrfast:discussion]
Subject: [mrfast:discussion] low percent mapping
Hi Michele
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
I used the repeat masked genome because this data is being analyzed for CNVs and SVs using mrCaNaVar and Variation Hunter. The online manual currently says to do this step in mrFAST if using mrCaNaVar. Is this still correct?
Thank you,
Michele
From: Can Alkan calkan@users.sf.net
Sent: Wednesday, March 23, 2016 2:16 AM
To: [mrfast:discussion]
Subject: [mrfast:discussion] low percent mapping
Hi Michele
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
yes, that is correct. Still, 35% mapping to repeatmasked genome is normal. The other alignment you have at 99% also includes common repeats, which, repeatmasking removes.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I'm aligning WGS data from a HiSeq and getting very low percent mapping, like 30-35% of the input reads? The bam file of the same fastq reads shows > 99% mapping. I've tried pe mapping with --best and single read mapping leaving that off and using -e 10, but it didn't change much. These are long reads, 250 bp, and I indexed the hg19 using --ws 13.
Any suggestions?
Thank you,
Michele
HI Michele,
Can you send the email to Can Alkan(calkan@gmail.com).
Thanks,
Farhad
Hi Michele
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
Can
Great,
Thank you for this information.
Cheers,
Michele
From: Can Alkan calkan@users.sf.net
Sent: Wednesday, March 23, 2016 2:16 AM
To: [mrfast:discussion]
Subject: [mrfast:discussion] low percent mapping
Hi Michele
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
Can
low percent mappinghttps://sourceforge.net/p/mrfast/discussion/946649/thread/3cc36e9b/?limit=25#e605
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I used the repeat masked genome because this data is being analyzed for CNVs and SVs using mrCaNaVar and Variation Hunter. The online manual currently says to do this step in mrFAST if using mrCaNaVar. Is this still correct?
Thank you,
Michele
From: Can Alkan calkan@users.sf.net
Sent: Wednesday, March 23, 2016 2:16 AM
To: [mrfast:discussion]
Subject: [mrfast:discussion] low percent mapping
Hi Michele
In your previous email you seem to map to repeatmasked reference. If you are still using the masked reference, 35% mapping rate is normal. You are removing ~50% of the reference anyway.
Can
low percent mappinghttps://sourceforge.net/p/mrfast/discussion/946649/thread/3cc36e9b/?limit=25#e605
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/mrfast/discussion/946649/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
yes, that is correct. Still, 35% mapping to repeatmasked genome is normal. The other alignment you have at 99% also includes common repeats, which, repeatmasking removes.