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User: raplayer

gravatar for raplayer
raplayer • 10
Reputation:
10
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New User
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Website:
https://github.com/rap...
Last seen:
1 year, 2 months ago
Joined:
4 years, 6 months ago
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p*************@gmail.com

Posts by raplayer

<prev • 12 results • page 1 of 2 • next >
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Tool: nanotimeparse - a bash solution for parsing oxford nanopore fastq on generation time
... As the title suggests, nanotimeparse is a new bash tool (only external dependency is GNU parallel) that parses an Oxford Nanopore fastq file on read generation times. You can git clone it here: https://github.com/raplayer/nanotimeparse Get subsets of (-i) Oxford Nanopore Technologies (ONT) basecal ...
long read fastq parsing tool time oxford nanopore written 14 months ago by raplayer • 10
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Phyloseq merge_sample error
... Sample merging a phyloseq object with merge_samples() hits an error but works for other objects But if I only take sample data from the phyloseq object by using sample_data() function on it, everything works fine... So my sample data merges but my phyloseq object refuses to... Information below: ...
microbiome metagenomics phyloseq written 3.7 years ago by raplayer • 10
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Comment: C: SEIR-SEI model in Python
... This is a great start for me Tonor. Thanks a lot for the links! ...
written 4.2 years ago by raplayer • 10
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SEIR-SEI model in Python
... Hey guys, I'm wondering if there is a library/package in python that implements the SEIR-SEI (suseptible, exposed, infected, recovered) model. If not, I'd appreciate any resources on the subject. Thanks! Robert ...
model sei seir seir-sei python written 4.2 years ago by raplayer • 10 • updated 17 months ago by sdlm • 0
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paired reads (headers) show up in 3 lines of sam file instead of expected 2
... **Problem:** Try to count features of sam file: htseq-count -m union -r name -t exon -i gene_id sorted1.mm10.sam mm10.gtf > sorted1.mm10.counts 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF line ...
alignment bwa mem sam written 4.5 years ago by raplayer • 10 • updated 4.5 years ago by Damian Kao ♦ 15k
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Comment: C: PE alignment with bwa aln and conversions
... Hey, yea bwa aln has an option to accept bam as input, but I do not see an option for this with bwa mem. ...
written 4.5 years ago by raplayer • 10
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Answer: A: PE alignment with bwa aln and conversions
... So the reason I wanted to get a fastq after alignment was so I could align the resulting aligned/unaligned reads to a different reference. My solution was to just use the bwa mem as u/igor suggested: bwa mem "index_prefix" "s1_R1.fq" "s1_R2.fq" > s1.sam samtools view -Sb -F0x4 "s1.sam" ...
written 4.5 years ago by raplayer • 10
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Comment: C: PE alignment with bwa aln and conversions
... That, and I was converting back to fastq so I could align to another reference. I see now that you can just use the bam file. ...
written 4.5 years ago by raplayer • 10
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Comment: C: PE alignment with bwa aln and conversions
... So to use sampe I need to align each read file separately? So I get an sai for R1, and another sai for R2? I had seen that you could just put both R1 and R2 in the argument list of bwa aln, but this results in only a single sai, which you would then use with samse. It's confusing... ...
written 4.5 years ago by raplayer • 10
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PE alignment with bwa aln and conversions
... So I've got paired-end read files: s1_R1.fq and s1_R2.fq 1. I align to some indexed reference with: bwa aln "index_prefix" "s1_R1.fq" "s1_R2.fq" > s1.sai 2. convert to sam: bwa samse "index_prefix" "s1.sai" "s1_R1.fq" "s1_R2.fq" > s1.sam 3. pull aligned reads only into bam format: sam ...
paired alignment samse sampe bwa written 4.5 years ago by raplayer • 10

Latest awards to raplayer

Popular Question 3.7 years ago, created a question with more than 1,000 views. For SEIR-SEI model in Python
Popular Question 3.7 years ago, created a question with more than 1,000 views. For paired reads (headers) show up in 3 lines of sam file instead of expected 2
Popular Question 3.7 years ago, created a question with more than 1,000 views. For PE alignment with bwa aln and conversions
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Phyloseq merge_sample error
Scholar 4.5 years ago, created an answer that has been accepted. For A: PE alignment with bwa aln and conversions
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