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Dear all,
I am using VarDict in a sample with known genotype. The sample was sequenced with an Illumina TruSight custom amplicon for BRCA1/2 on a MiSeq sequencer.
We know it has a deletion of 70bp…
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Dear Luca Pinello
I am using CRISPRessoPooled.py script to analyzed the paired ends reads data by Illumina.
the read length is 150 bp.
the amplicon size is 180bp long.
below is the command that I…
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Spin out from in-person discussion on #43, it would be interesting to apply primer trimming based on the actual primer sequences as a possible alternative to hard-coded left/right cutting, or looking …
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Dear Daniel,
I am trying to do taxonomy classification using KrakenUniq with the PR2 database.
In order to build a custom KrakenUniq database, a taxonomy database, specifically nodes.dmp and names…
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Hello,
I'am using GroupReadsByUmi followed by CallMolecularConsensusReads on personal paired-end data;
in some amplicons, paired reads overlap and even overhang, eg the 3'end of the reverse read end…
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Hello,
Hello, I am trying to use Nanopolish v.11.0 on the Flux Linux-based operating environment at the University of Michigan to polish assembled contigs from Canu v1.8 of demultiplexed amplicons …
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I deduplicated my files in `bismark`:
> The script deduplicate_bismark is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-en…
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Environment: CentOS6.5, Python 2.7.11, CRISPResso installed from source (master.zip downloaded from github), needle, flash and trimmomatic are in the CRISPResso dependencies dir.
Data was downloaded…
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Hello.
I am using ampliCan with 450 bp reference sequence and 2 x 300 bp data set. Unique reads decreased to about 70% compared with Good reads. Even when compared with the result from CrispRVariants…
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Dear Jared,
I would like to know if there are any plans to add a vcf2fasta option for filtering out variants based on quality score (QUAL field) in the vcf file produced by nanopolish.
Thanks in adv…