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Hello,
I'm working on 10X reads from a non-model organism with around 13,000 contigs in the reference and was wondering which aligner would be recommended after running Longranger basic.
Thanks!
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I believe there should be updates to the README:
> Please contact us if you're interested in using Lariat independently of the Long Ranger pipeline.
The easiest way to do this is as follows:
…
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Dear Peter,
We were hoping that hapCUT2 would allow us to skip LongRanger to phase variants. However, we are running into some issues, and I would like to check back with you regarding some questio…
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Hi,
I wanted to have your opinion on using purge_dups with 10X genomics data.
Have you tried to run it with such data?
For the mapping of the reads, do you think it is best to use the `longranger…
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Hi, we are trying to align some 10x reads to a PacBio reference that consist of 4000 scaffolds. We would like to know if EMA has any constraint regarding the size of the reference as LongRanger has (1…
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Hello,
I'm super excited to test this tool out. I'm currently testing it out with the LongRanger output and the 10X-specific TitanCNA workflow. I keep getting this error message when one of the SVs…
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> Alevin adopts efficient algorithms for cellular-barcode whitelist generation, cellular-barcode correction, lightweight per-cell UMI deduplication and quantification.
Is it possible to use Salmon …
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Say you are only given a longranger processed BAM file that you would like to use for other purposes. Many tools cannot use BAM format directly. It could be useful to support a fast SAM/BAM conversion…
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Dear author,
I would like to use Emerald to align my 10X genomics reads to a reference.
After reading the README and the issues page I am confused about the following things:
1. What input i…
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I've aligned reads to a de novo assembly using BWA-MEM rather than Long Ranger align. The BWA alignments have the `BX` tag but no `MI` tag. Would you consider implementing a module to group together n…