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### Description of the bug
When using `--aligner cellranger` the matrix files are not read correctly by `ReadMtx` but are read correctly by `Read10X`.
```
Command error:
Attaching SeuratObject
E…
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Dear PBSIM3 maintainers,
I am YU Zhejian from the Zhejiang University-University of Edinburgh Institute. Our group has been using PBSIM1/2/3 to simulate long-read RNA-Seq reads (with [YASIM](https:…
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Hi,
I am currently learning to use MitoHPC to analyze WGS data. After successfully setting up the environment and testing it according to the tutorial, the script did not perform the analysis or prod…
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Hi,
I was testing the inc-seq.py script with your data "inc_seq_test_read.fa", however, I keep getting the same error, please see below. I was not able to find online any module named 'aligners'. W…
ghost updated
3 years ago
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Hi,
I am trying to align paired-end HI-C data with bwa-mem2 but it seems there is an issue with header. Here is the command i used:
bwa-mem2.avx512bw mem -5SP -T0 -t50 -R "@RG\tID:E003868R:379:GW2…
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We are currently using default settings for each of the aligners. This is a good starting point as needed for illustrating how the tools perform out-of-the-box. As the defaults vary widely, in the nex…
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We will need to perform quality control on sequencing reads, `BAM` files generated by aligners and alignment statistics output by aligners.
Use the small `BAM` file provided at the following [link…
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Hi Adrian,
Using an aligner such as STAR or Tophat seems to give more alignments/content from indrop sequence reads compared to the current Bowtie aligner usage. Would it be possible to incorporate…
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Hi!
We found a BAM file, produced by Isaac 03.16.02.19, that contains BC tags with "none" value, which is invalid according to the [standard](https://github.com/samtools/hts-specs/blob/master/SAMta…
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Looks like in some circumstances the output is not sorted by read name. Technically speaking I think this is fine (the output is still valid .sam as far as I can tell), but read-name sorting is requir…