User: Buffo

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Buffo340
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Posts by Buffo

<prev • 129 results • page 1 of 13 • next >
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Comment: C: MiRNA orthologues between human and chick
... I would call them "conserved" more than orthologues, I THINK it is more appropriate. ...
written 6 hours ago by Buffo340
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Comment: C: Reference guided assembly of contigs
... For a very close related species SPADES works even better and faster than IDBA_hybrid. ...
written 1 day ago by Buffo340
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Comment: C: Reference guided assembly of contigs
... 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 Buffo340
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Answer: A: Getting average fragment length for single end reads
... [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 Buffo340
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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 Buffo340
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Comment: C: How to download raw data in batch from NCBI based on Series Accession number or
... This may be helpul [batchentrez][1] [1]: https://www.ncbi.nlm.nih.gov/sites/batchentrez ...
written 4 days ago by Buffo340
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Comment: C: SPAdes: <jemalloc>: Error in malloc(): out of memory
... 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 Buffo340
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Answer: A: extracting sequences from a fasta file
... 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 Buffo340
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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 Buffo340
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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 Buffo340

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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