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Not much Nanopore data has been run using the pipeline, so it's hard to say how appropriate the default parameters are for these data vs Illumina. However, some suggestions based on the [`setDadaOpt`]…
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Hi,
We have some tools that expect to see allele depths in FORMAT column (ie A,C,G,T or AU,CU,GU,TU) and TIR/TAR for indels. Would be great if there was a way to get these in the vcf output.
Tha…
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### Description of feature
Hi,
Illumina has introduced a new read compression format, ORA: https://www.illumina.com/science/genomics-research/articles/design-ora-lossless-genomic-compression.htm…
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**Is your feature request related to a problem? Please describe.**
When trying to analyze nanopore sequencing data with CRISPResso2, the runs fails due to insufficient memory. I believe this is arisi…
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Hi,
I am hoping to perform transcriptome assembly using both nanopore long read sequencing data and illumina short read sequencing data. It appears RATTLE only permits the use of long read sequenci…
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Dear all,
I have Illumina data (150 *2 bp), in total, 110 Gb. I cleaned it with Trimmomatics. I used Genomescope to estimate the genome size with kmer = 21. The estimated genome size is about …
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My problem is that I am having difficulty obtaining a list of variants using bcftools mpileup and bcftools call with PacBio data. I do not have this problem with data of Illumina paired-end sequencing…
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Hi
Thanks for a great method.
I'm working on chromosome contact data generated from a long read sequencing method. Check link here if interested:
https://www.biorxiv.org/content/10.1101/833590v1…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…
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`KLSampleSheet` includes the property:
```
sections = (_HEADER_KEY, _READS_KEY, _SETTINGS_KEY, _DATA_KEY,
_BIOINFORMATICS_KEY, _CONTACT_KEY)
```
I would love to know if th…