Tom Morrison
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Latest activity by Tom Morrison-
Tom Morrison commented,
Hi Bhanu, Two example read pairs are in my first post. Both of their fastq R1 & R2, their bam output from markduplicates, and their appearance in IGV. Their 5-prime sequences are identical (their...
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Tom Morrison commented,
Hi Bahnu, using non spark MarkDuplicates did not alter the results. Removing the --optical-duplicate-pixel-distance 2500 argument did not alter the result. Have you attempted to reproduce the resu...
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Tom Morrison commented,
Hi Tiffany, I uploaded the zipped file: MD_Issue_200701.zip, the contents are: Files created from markDuplicates; AgilentMale-BL-R-1-B-190508_S1_MD.bam, AgilentMale-BL-R-1-B-190508_S1_marked_dup_m...
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Tom Morrison commented,
Hi Tiffany, Above, I kept writing FASTA when I meant FASTQ. Also, I did not see a way to configure BWA to output the align reads independently. Do you know what setting I would use? Alternativel...
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Tom Morrison commented,
I've never outputted separate reads from bwa, I'd have to look into this if this is what you want. The FASTA rows in my original post do have read 1 and 2 for these querynames.
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Tom Morrison commented,
Hi Tiffany, I've pasted the pre mark duplicate bam reads for the requested querynames below. The FASTA and markduplicate reads for these querynames was in my original post. NB551226:81:H273NBGXB:3...
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Tom Morrison commented,
Hi Tiffany, Unfortunately, neither of those options eliminated the duplicates.
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Tom Morrison created a post,
MarkDuplicatesSparks not removing some duplicates?
I'm attempting to remove duplicates for some TST170 sequences but end up with what appear to be identical read sequences. For this sequence run, the PCR duplicates were quite high (21K) with MarkD...