User: raplayer
raplayer • 10
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Posts by raplayer
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... 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 ...
written 14 months ago by
raplayer • 10
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... 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:
...
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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... 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 ...
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... **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 ...
written 4.5 years ago by
raplayer • 10
• updated
4.5 years ago by
Damian Kao ♦ 15k
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... 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
1
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... 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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... 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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... 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
3
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... 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 ...
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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