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Hi
I am trying to do fusion neoantigen prediction using Arriba, however STAR can't cope with long reads and ideally STARlong should be used - do you think this will be able to be supported please?
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Hi,
I have 51bp PE RNA-seq libraries from FFPE tissues.
The raw fastq shows considerable adapter contamination and some over represented sequences, mostly mapping to ribosomal gene sequences.
…
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can the use of long genomic reads improve the accuracy ?
tnx !!
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Hi,
My question is as the title. I used STAR to map single-end RNA reads to reference. And my final.out is like below:
Number of input reads | 314991228
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Hi Alex,
I ran the following command
STAR-2.7.10a/source/STAR --readFilesCommand gunzip --quantMode TranscriptomeSAM --outFilterMismatchNmax 999 --sjdbGTFfile /home/elkree01/RNAseqAug2022/Hom…
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## Problem description
Currently (version 0.2.0-beta2), `flye_end_repair.sh` is run after the assembly step to fix any potential issues with the region around the ends of circular contigs. At the end…
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@mbhall88 noted a potential problem with the `--max_covg` parameter that can affect `pandora map` and `pandora compare`: unmapped reads enter the coverage calculation although they do not contribute f…
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Even when you choose paired end data files this is not passed to minimap2 correctly.
https://github.com/lh3/minimap2#map-short-accurate-genomic-reads
"Two reads are considered to be paired if th…
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```
Hi,
I'm trying to figure out how to run a second mapping pass, as described in the
paper
"It is also possible to run a second mapping pass, supplying it with splice
junction loci found in the …
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Hi ! I would like to run findAlleles to continue the analysis of SHM. However, when I run the findAlleles command with my own data which generated from analysis, no clone information is detected in by…