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I am trying to use xHLA on WES data, however I am not getting the same typing results as with Athlates. I have been previously aligning WES reads to the whole hg38 genome and am about to try aligning …
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TODO: Fix the 28-bit limit on CIGAR length size in the internal memory structures.
While we have no immediate plans to support reads several Gb long, we do support references this long now.
Howe…
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Hello,
So, I used STAR to align some whole-genome sequences and for the alignment it seemed to work very well. However, when I use the resulting BAM files for coverage statistics with picard it tak…
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Hi!
Can CHOP be used to do the actual read mapping, or does it just create a fasta file that I e.g will need to index with BWA and then map reads to? If so, I assume my final alignments will be rel…
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# OGS remapping and manual annotations
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# Change old content
- [ ] back up and deprecate ol…
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Hi all,
I was running `lexicmap search` with the parameters recommended in the tutorial, and for one fasta I received this error message
```
Panic: runtime error index of out range [X] with len…
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Hello,
I am trying to do the alignment pipeline from fastq files that I got for whole exome sequence.
I first used trim_galore to remove adapaters and I got .fq files.
Then I downloaded the human…
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Thanks for the good material. I have a question about the alignment using bowtie2, here according to [`mutation_sequencing_analysis_script.sh`](https://github.com/aldob/iMUT-seq/blob/4476db76f2058d0af…
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The webpages (https://sanger-pathogens.github.io/Roary/) said We cannot use the output of Roary as the input to Gubbins, do you mean the "core_gene_alignment.aln" file cannot be used as the input to G…
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Hi,
We have constructed genomes for our 18 Mtb samples, by mapping PacBio sequencing data to the Mtb reference H37Rv using SMRT Link v 2.3.0.140936. Lineages of these samples have been experimental…