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Dear all,
Recently, I used STAR to align reads from the RIC-seq library. In theory, RIC-seq reads consists of three segments: leftArm + "C" + rightArm (C is cytosine). During the library preparati…
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We use STAR Solo to map results of CRISPR screens, specifically at one of the steps we map guide RNA reads that we have introduced and assign them to cells . For that we generate artificial reference,…
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Hello,
I've been mapping paired end reads to a graph built with minigraph-cactus
```
vg giraffe --progress --fragment-mean $frag_mean --fragment-stdev $frag_stdev -Z ${inDir}/arenosa_pg.d2.gbz …
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I am working on a CRISPR data treated by two sgRNAs and sequenced with targeted sequencing. The distance between the two sgRNA is 3000bp which is much longer than amplicon. The targeted area is the w…
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Hello,
I wonder if there are guidelines regarding number of reads (or pairs) to get from sequencing for non-human Cut&Run experiments?
I'm working on a diatom species (~28M bp genome) and 10 mil…
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Hi everyone!
I am polishing a Nanopore assembly with Illumina short reads via pilon. On one contig, it is assumed to be two inversed repeats. As illustrated by the variable scale in the coverage plo…
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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
…
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```
I have been using STAR with Illumina 101bp paired end reads. The first set of
libraries I sequenced work great going through the pipeline, but I have had a
very strange problem with the most rec…
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Hi Alex,
I am using STAR for RNA-seq read alignment fro the datasets from both the same species (regarding the reference genome) and out-group species (with around 2% of sequence divergence to re…
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Hi all,
I am trying out Magic-BLAST for mapping short-reads, and may want to test it in various pipelines.
I noticed, however, that the MAPQ field in the SAM output is either 0 or 255.
At fir…