User: Pavel Senin
Pavel Senin • 1.8k
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Posts by Pavel Senin
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Comment:
C: randomly shuffle BAM file
... good point, will `sort --random-sort` do the job? (but it'll be slow...)
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written 2.8 years ago by
Pavel Senin • 1.8k
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7
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Comment:
C: randomly shuffle BAM file
... I would use `shuf` for shuffling alignment lines taking care about header: detaching it before and reattaching it after
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written 2.8 years ago by
Pavel Senin • 1.8k
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2
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... Hi David: thank you for this excellent example! Right now I am trying to make use of the local SRAdb without much online querying, if not working, that shall be a next step.
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written 3.1 years ago by
Pavel Senin • 1.8k
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... Hi guys:
I wonder how to get links for FASTQ files using Bioconductor SRAdb package for specific taxons and tissues? Currently I am trying to get through by using JOINs and fulltext searches with LIKE, but it is so slow to figure it out..., maybe someone already has solved that?
Thanks!
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written 3.1 years ago by
Pavel Senin • 1.8k
• updated
3.0 years ago by
Lynxoid • 210
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... also accepted. XML is a better way to get data, parsing/debugging it is the pain though.
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written 3.1 years ago by
Pavel Senin • 1.8k
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1.1k
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2
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... That works, but you also need to divide by 2 for paired-end libraries :)!
...
written 3.1 years ago by
Pavel Senin • 1.8k
4
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2
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1.1k
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... Hi folks:
I am trying to get raw RNASeq data from ENA and wonder how to know the length of the sequences in those FASTQ files without downloading them?
In the query design I follow their guide, and use the "nominal_length>XXX" in the query, but this filtering mechanism doesn't work...
Than ...
written 3.1 years ago by
Pavel Senin • 1.8k
• updated
3.1 years ago by
Chris S. • 270
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2.9k
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5
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... This article may help you. It has a table of tools and approaches. I am not affiliated with these guys.
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written 3.3 years ago by
Pavel Senin • 1.8k
0
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2
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2.4k
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answers
... Likely, there is no way to provide a list of nodes as a parameter. I would approach this via pruning the tree instance by splicing not-needed nodes out at first and computing the sum second. But I am not sure how well this will preserve the branches lengths (however that manual says it does with "-p ...
written 3.3 years ago by
Pavel Senin • 1.8k
0
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2
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2.4k
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2
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... I believe that bioPerl has that solved, bioPython may help too, for the total length they have a built-in method:
my $total_length = $tree->total_branch_length;
...
written 3.3 years ago by
Pavel Senin • 1.8k
Latest awards to Pavel Senin
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For Is there a way to know sequences length when querying ENA programmatically?
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For Rsamtools & Iranges, Getting Junction-Aware Coverage
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For Snp Format For Gff3: 'Name=' Vs 'Id='
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12 months ago,
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For Stress Response: is there a mapping between KEGG and COG? [solved]
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For C: How to extract unique mapped reads from your bam files?
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For Snp Format For Gff3: 'Name=' Vs 'Id='
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For C: How to extract unique mapped reads from your bam files?
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For Rsamtools & Iranges, Getting Junction-Aware Coverage
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For Rsamtools & Iranges, Getting Junction-Aware Coverage
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For Pauda (Bowtie) Exception While Processing Microbial_Refseq
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For A: How To Identify The Protein Domains Of A Specific Protein?
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For C: Problem With Perl Script When Extracting Sequences According To The Ids
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For C: Problem With Perl Script When Extracting Sequences According To The Ids
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For A: How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frame
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