User: rmf
rmf • 500
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Posts by rmf
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Answer:
A: PacBio merge runs
... I managed to get it to work. Not sure if this is the best way.
I converted `*.bax.h5` to BAM separately for each run.
bax2bam -o "sample1_run1" $(find . -name "*.bax.h5")
bax2bam -o "sample1_run2" $(find . -name "*.bax.h5")
This creates scraps and subreads BAM files. I merged the subread ...
written 4 weeks ago by
rmf • 500
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... For one of my samples, I have two runs.
sample1
+-- run1/
| +-- *.bax.h5
+-- run2/
+-- *.bax.h5
My workflow involves using **bax2bam** to convert *.bax.h5* to *unaligned bam*. Then using **pbalign** to convert *unaligned bam* to *aligned bam*.
How do I combine these two ...
written 5 weeks ago by
rmf • 500
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... How exactly does one use the XML file? At what point and where? ...
written 5 weeks ago by
rmf • 500
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... For fast LD computation directly from a VCF file, see [here](https://www.biostars.org/p/347796/). ...
written 11 weeks ago by
rmf • 500
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6 follow
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... Fast LD computation from a VCF file using **vcftools**, **bcftools** and **tomahawk**. Install **tomahawk** from [here](https://github.com/mklarqvist/tomahawk).
Following commands are run on the Linux command-line.
For LD computation, pairwise comparisons are performed between all SNPs, therefore ...
written 11 weeks ago by
rmf • 500
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... You are right. I don't use it here. The `mid` variable is just used to find the mid point of the interval windows. When plotting, you could use `mid` instead of `start`. That was my plan, but then it turns out, it doesn't make much difference for this particular plot. ...
written 12 weeks ago by
rmf • 500
0
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1
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140
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1
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... I think `wc -m` counts the newline characters as well. What we actually want is `total_chars - newline_chars = bases`. ...
written 3 months ago by
rmf • 500
0
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1
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140
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1
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... Ah right! Ensembl count for human is based on the primary assembly. And some organisms don't have primary assemblies, just the top-level. ...
written 3 months ago by
rmf • 500
1
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1
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140
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1
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... I am calculating the total genome length from a fasta file using the following code
`zcat genome.fa.gz | grep -v ">" | wc | awk '{print $3-$1}'`
For [Yeast](ftp://ftp.ensemblgenomes.org/pub/fungi/release-41/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz), ...
written 3 months ago by
rmf • 500
• updated
3 months ago by
Nicolas Rosewick ♦ 7.2k
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... Well.. Your error message says your input fastq file is not in gzip format. In that case you have to modify the script to accept non-gzipped fastq files. Change `zcat` to `cat`. That's as far as I can see. ...
written 3 months ago by
rmf • 500
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