User: Buffo
Buffo • 340
- Reputation:
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Posts by Buffo
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... I would call them "conserved" more than orthologues, I THINK it is more appropriate. ...
written 6 hours ago by
Buffo • 340
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... For a very close related species SPADES works even better and faster than IDBA_hybrid. ...
written 1 day ago by
Buffo • 340
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... spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly ...
written 1 day ago by
Buffo • 340
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... [Prinseq][1] and [biopieces][2] mainly
[1]: http://prinseq.sourceforge.net/manual.html
[2]: https://github.com/maasha/biopieces/wiki/HowTo ...
written 1 day ago by
Buffo • 340
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Comment:
C: align fasta files using bowtie2
... First:
bowtie2 -p 8 -x index_file -f fasta_reads.fasta -S result.sam
Then,
$ samtools view -bS result.sam > file_out.bam
$ samtools sort file_out.bam file_.sort
$ samtools index file_.sort
And finally load the bam final in IGV to visualize it (after load your fasta refe ...
written 4 days ago by
Buffo • 340
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... This may be helpul [batchentrez][1]
[1]: https://www.ncbi.nlm.nih.gov/sites/batchentrez ...
written 4 days ago by
Buffo • 340
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... It depends basically of: How much reads do you have? How long is your genome expected to be? and, in the case of spades, which and how many kmers are you using?, [spades_manual][1]
`you may try: -k 21,33 --careful --only-assembler`
[1]: http://spades.bioinf.spbau.ru/release3.5.0/manual.html ...
written 4 days ago by
Buffo • 340
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... This is my python script to do that, save it as sequence_extractor.py and run it :)
#!/usr/bin/env python
#-*- coding: UTF-8 -*-
from __future__ import division
import sys
########################################################################################## ...
written 5 days ago by
Buffo • 340
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Comment:
C: How to assemble contigs?
... In adition, if you have a very close related specie (to genomic level) with a complete assembled genome, you can use it as reference to assembly your reads (spades or idba_hybrid; in linux by command line). But with paired end reads it would be very difficult (or even imposible). ...
written 6 days ago by
Buffo • 340
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Comment:
C: blastn for very short sequences
... in fact for very short sequences botwtie (v1) is the best option rather than bowtie2 because it allows mismatches :). ...
written 7 days ago by
Buffo • 340
Latest awards to Buffo
Scholar
25 days ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Centurion
29 days ago,
created 100 posts.
Scholar
4 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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