-
```
hi, I use stamtools to deal with SAM form mosaik-aligner to find mutations.
and when i used the command :
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100
> flt.txt…
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Dear team;
Thanks for providing those wonderful reference genome. It helps me a lot in my research. I met a problem that many of my reads could mapped to rrna region but was classified to not aligned…
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Hi,
I did bs3-build as "./bs3-build -f ./reference_genome/Sscrofa11.fa --aligner=snap". This command went well.
However, I can not find the index file in "./reference_genome/Sscrofa11.fa_snap/W_G2A …
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Hello,
I would like to use BrumiR to identify small RNAs in a species without a reference genome (thanks for developing BrumiR), but get the following error during compilation:
~/brumir$ make al…
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Tried to run dragmap, the commands are:
` dragen-os -r /paedyl01/disk1/yangyxt/indexed_genome/hg19 -1 /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/forward_read/TCA-082A-54…
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Study the code for alignment in bowtie2, and see how we can modify it to our greedy algorithm.
- [ ] #12
- [ ] Modify the two functions and fill `score` with penalty calculated by the greedy algor…
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I'm trying to use your tool to annotate another sequence (both can be found on NCBI):
```
annotate-genome.py --reference FR682468.2.gb --genome MH681419.1.fasta --aligner mafft
```
However, I ke…
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Hi,
I was trying to process blood samples using STAR diploid, and the aligner seems to fail on subset of samples. We notice that these samples had paired-end reads
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Hi,
Could you plainly explain how a golden BAM is generated? I’ve noticed that the BAM file obtained using fq files and BWA differs significantly from the golden BAM.
Thanks
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Hi, thanks for this fast and easy-to-run aligner :) I have two questions.
1. How the "coverage" in the report was calculated? I had a coverage value 0.95 from a human GRCh38 to human T2T alignme…