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When I try to run the example files the program crashes when it tries to use picard, it might be something with the input file it cannot find. It only produces an empty sample.bam output file before i…
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Hi,
I would really like to try out your analysis method but am having a problem with running the test data. When running the dafga_refDB.py script I get the following error:
dafga_refDB.py -gp pmoA_…
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Hello,
I used mutect2, vardict, and varscan to call variants on matched tumour-normal bam files containing reads that were UMI-collapsed with fgbio's CallDuplexConsensusReads and stitched using ill…
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Hello!
I am using cutadapt to demultiplex my reads (v2.10 with Python 3.7.6).
Basically, I have a pair of fastq files (e.g. input_R1_001.fastq and input_R2_001.fastq) which contain sequences fro…
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Hello there,
thank you very much for designing such software, it is very useful!
I just have to understand a couple of things regarding it:
1) is it possible to specify the lenght of foward and rev…
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Hello.
I'm checking the files for download and I see some file with name "refseq207nr_classifierpairA.qza", are this files for use with qiime2? Why are there classifierpairB and C?
What is the c…
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Hi @benjjneb,
I've been processing some old amplicon sequencing sets with dada2 recently with no trouble (I'm a big fan) . However the last set of paired reads seems to have a mix of primer orienta…
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Hi everyone,
I encounter an unexpected behavior of `seqkit amplicon`: `seqkit amplicon -p` returns a different result than `seqkit amplicon -F -R`.
seq.fasta
```
>seq1
ATGCGCTATATATATTTT
>se…
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In the exercise, the code fails when executing:
```
primer_df, blat_df = AnoPrimer.designPrimers(
species='gambiae_sl',
assay_type='qPCR primers', # assay_type options are: 'qPCR pr…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…