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When running `extract-sv-reads` on a long-ranger aligned BAM file, the program quits immediately with the following message:
```
ERROR: Error parsing position from SA tag hs38d1,-1,-,42S108M,0,15
…
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I have a custom MultiQC module called `target_phasing`, which can be found [here](https://github.com/lumc/multiqc_pgx). It runs in MultiQC v1.11 and before, but not in MultiQC v1.12 or later. The modu…
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Hi,
I am running the NAIBR to find structure variants.
Here is the error I get from the program.
Traceback (most recent call last):
File "NAIBR.py", line 6, in
from get_reads import…
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Relates to #6.
As noted in the longranger [docs](https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/bam) (below) the suffix number can be any integer, not just "-1", as i…
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Hi,
I was trying out LEVIATHAN for calling variants on a .bam file produced with LongRanger on linked-reads fastq files (TELL-seq technology). I have successfully built the LRez barcode indexes, but …
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Hi there,
I'm running break10x on my cluster as follows:
/nfs/research1/marioni/claumer/Scaff10X/src/break10x -nodes 40 -gap 100 -reads 5 -score 20 -cover 50 -ratio 15 /nfs/research1/marioni/cla…
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The 10X dataset that I would like to use with EMA appears to have an 8 bp index instead of 16. Do you know where I can find an 8 bp whitelist?
Thanks,
Michael
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# Linked-Reads QC: Summarize sequencing library quality of 10x Genomics Chromium linked reads
The goal of this project is to develop a software tool to quickly report on the quality of a 10x Genomi…
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Hello,
I have a more methodological question - I am dealing with a partially collapsed diploid plant genome assembly.
I did my phasing using 10x data (see issue #262) but now I realized that most …
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Hi, I run `arbitr.py -i pilon.fasta pilon.bam -m 75000 -s 40000 -B 20 -F 70 -Q 60 -n` 3 and it leads to this error. Could you please help me? Thank you very much.
```
$ arbitr.py -i pilon.fasta …