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Hi Heng,
Always interested to test out new software that you put out. I am doing a lot of targeted resequencing with Illumina TruSight Amplicon data of tumour-only samples. I have been looking for so…
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We need to do a bead size selection clean up to remove primer dimers from our pooled PCR product for ITS2. Details of the amplification and prep for these samples are in my [notebook post](https://ahu…
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Hello,
I am interested to confirm an allele frequency for a SNV in BRAF gene using amplicon sequencing data. The length of amplicon is 271bp, and paired reads are 101X2. So there is a gap between t…
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Dear Developers,
I'm trying this pipeline. However, when I typed
python ./scripts/Master.py -h
, it turned out:
Traceback (most recent call last):
File "./scripts/Master.p…
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extracting the 16S rRNA gene and doing an OTU clustering will illustrate the diversity captured with targeted amplicon sequencing
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Hi,
I have Nanopore sequencing data for the 16s gene of microbioal communities. Can dada2 be used for this type of sequencing data, and if not, is it in development? Thanks!
Best wishes,
Carla …
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Hi,
I am attempting to run your code on targeted sequencing data from an S5 instrument that has probes across multiple chromosomes. For your probe information file there are required sections for G…
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User is seeing non-ref blocks with GQ=0 even though bamout shows reads covering that region. Example: chr1 14155446 . C . . END=14155446 GT:DP:GQ:MIN_DP:PL 0/0: 100:0: 100 :0,0,0
Discussed this at…
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Currently we generate the mapping files for an amplicon run with the `amplicon-pooling.ipynb` notebook, however this should be changed to work the same was as with metagenomics runs. Namely using the …
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Hi, I'm a new to cnvkit. Thanks for this excellent tool. As it was pointed out in the documentation, CNVkit is primarily designed for use on hybrid capture sequencing data, where off-target reads are …