User: v.berriosfarias

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Posts by v.berriosfarias

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Filter contigs by size: Different output between quast report and python output
... Hello Dave, iḿ trying to use your code for filtering some contigs, but I got a identation error message: > File "contig_length_filter.py", line 2 long_contigs = [] ^ IndentationError: expected an indented block so I suppose that I must add something on the double brackets? Regards : ...
written 12 hours ago by v.berriosfarias10
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Comment: C: Filter contigs by size: Different output between quast report and python output
... for what "SeqIO.parse" stands for? (trying to understand the command) I'm trying to filter contigs so this code can help me. ...
written 17 hours ago by v.berriosfarias10
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On read sequencing libraries, the opposite strands are considered on the files? (and how are they handled on assembly?)
... Just want to know if on my paired end reads fastq files are considered the opposite strand, Does on the sequencing procedure the opposite DNA strands discarded or are they sequenced too? if the are sequenced, how are the opposite DNA strands handled on contig assembly steps? ...
reads assembly sequencing written 4 days ago by v.berriosfarias10
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fastp issue (trimming and read filtering tool)
... Hello, has anyone used fastp? I used it for trimming metagenomic libraries , the issue is that I used as input a file with 40M sequences and the output was a file with 11M sequences. the filtering results des not give detail of what happened with the removed sequences , although there is a report t ...
trimming adapter fastp written 23 days ago by v.berriosfarias10
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Comment: C: How to extract a sequence below a fasta header (">") from a fasta file ?
... this was very useful , thanks so much! ...
written 6 weeks ago by v.berriosfarias10
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Comment: C: How to extract a sequence below a fasta header (">") from a fasta file ?
... can you explain the $0 and the $1 on this situation ? I'll be so grateful if you explain this ...
written 6 weeks ago by v.berriosfarias10
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Comment: C: How to extract a sequence below a fasta header (">") from a fasta file ?
... yes , this worked for me thanks so much :) ...
written 6 weeks ago by v.berriosfarias10
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K-mer usage in metagenome assemblies
... Hello just want to ask what should be the considerations at choosing a specific k-mer size on metagenome assemblies pipelines (particularly based on de Bruijn graphs)? I have read an issue here https://github.com/ablab/spades/issues/251 where coverage seems to be a great determinant on the k-mer cho ...
k-mer assembly metagenomics written 6 weeks ago by v.berriosfarias10 • updated 6 weeks ago by Rayan Chikhi1.5k
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How to extract a sequence below a fasta header (">") from a fasta file ?
... Hello I have a lot of sequences in a FASTA file, and I want to extarct a specific sequence knowing the header ID. for example the header of a sequence is: NODE_19_length_5758_cluster_19_candidate_1 I know that with `grep` I can extract the header, but i want the below sequences to appear on stdout ...
fasta bash written 6 weeks ago by v.berriosfarias10 • updated 6 weeks ago by ATpoint45k
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Comment: A: Is it possible to work with paired-end reads for assembly purposes using metaspa
... damn, thanks I read that on the github page : https://github.com/ablab/spades#meta maybe the info there is not actualized, thanks so much ...
written 8 weeks ago by v.berriosfarias10

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