User: Pavel Senin
Pavel Senin • 1.9k
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- Los Alamos, NM
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- http://seninp.github.io/
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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...)
...
written 3.9 years ago by
Pavel Senin • 1.9k
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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 3.9 years ago by
Pavel Senin • 1.9k
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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 4.3 years ago by
Pavel Senin • 1.9k
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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!
...
written 4.3 years ago by
Pavel Senin • 1.9k
• updated
4.2 years ago by
Lynxoid • 220
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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 4.3 years ago by
Pavel Senin • 1.9k
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... That works, but you also need to divide by 2 for paired-end libraries :)!
...
written 4.3 years ago by
Pavel Senin • 1.9k
4
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2
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1.4k
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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 4.3 years ago by
Pavel Senin • 1.9k
• updated
4.3 years ago by
Chris S. • 290
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5
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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.
...
written 4.5 years ago by
Pavel Senin • 1.9k
0
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2
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3.2k
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2
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 4.5 years ago by
Pavel Senin • 1.9k
0
votes
2
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3.2k
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2
answers
... 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 4.5 years ago by
Pavel Senin • 1.9k
Latest awards to Pavel Senin
Appreciated
12 months ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Is there a way to know sequences length when querying ENA programmatically?
Good Answer
16 months ago,
created an answer that was upvoted at least 5 times.
For A: Superimpose 2 Heatmaps
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19 months ago,
created a question with more than 1,000 views.
For Is there a way to know sequences length when querying ENA programmatically?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Snp Format For Gff3: 'Name=' Vs 'Id='
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Stress Response: is there a mapping between KEGG and COG? [solved]
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2.6 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Snp Format For Gff3: 'Name=' Vs 'Id='
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3.2 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Pauda (Bowtie) Exception While Processing Microbial_Refseq
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3.9 years ago,
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For A: How To Identify The Protein Domains Of A Specific Protein?
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4.1 years ago,
created a comment with at least 3 up-votes.
For C: Problem With Perl Script When Extracting Sequences According To The Ids
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4.2 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
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For C: How to extract unique mapped reads from your bam files?
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For A: Stress Response: is there a mapping between KEGG and COG? [solved]
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4.8 years ago,
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For A: How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frame
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5.0 years ago,
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For A: Bwa Mem Have Different Alignment Result When Using Different Threads
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5.0 years ago,
created a comment with at least 3 up-votes.
For C: Problem With Perl Script When Extracting Sequences According To The Ids
Scholar
5.0 years ago,
created an answer that has been accepted.
For A: Stress Response: is there a mapping between KEGG and COG? [solved]
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5.3 years ago,
created a post with more than 5 votes.
For A: How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frame
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5.3 years ago,
created a post with more than 5 votes.
For A: Bwa Mem Have Different Alignment Result When Using Different Threads
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