User: rmf

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rmf500
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Posts by rmf

<prev • 123 results • page 1 of 13 • next >
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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 rmf500
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PacBio merge runs
... 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 ...
assembly pacbio written 5 weeks ago by rmf500
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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... How exactly does one use the XML file? At what point and where? ...
written 5 weeks ago by rmf500
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... For fast LD computation directly from a VCF file, see [here](https://www.biostars.org/p/347796/). ...
written 11 weeks ago by rmf500
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Tutorial: Fast LD computation from VCF files using tomahawk
... 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 ...
bcftools ld vcf tutorial snp vcftools written 11 weeks ago by rmf500
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... 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 rmf500
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Comment: C: Fasta length does not match Ensembl info
... 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 rmf500
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Comment: C: Fasta length does not match Ensembl info
... 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 rmf500
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Fasta length does not match Ensembl info
... 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), ...
fasta annotation written 3 months ago by rmf500 • updated 3 months ago by Nicolas Rosewick7.2k
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Comment: C: bwa mem: Passing a variable to read group
... 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 rmf500

Latest awards to rmf

Popular Question 26 days ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 4 weeks ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
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Scholar 5 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
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Scholar 9 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
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Scholar 11 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Scholar 11 months ago, created an answer that has been accepted. For A: Regenotype vcf using some samples as reference
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
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