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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- Joined:
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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 5.0 years ago by
Pavel Senin • 1.9k
0
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7
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4.9k
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7
answers
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 5.0 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 5.3 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!
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written 5.3 years ago by
Pavel Senin • 1.9k
• updated
5.2 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 5.3 years ago by
Pavel Senin • 1.9k
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1.6k
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2
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... That works, but you also need to divide by 2 for paired-end libraries :)!
...
written 5.3 years ago by
Pavel Senin • 1.9k
4
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1.6k
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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 5.3 years ago by
Pavel Senin • 1.9k
• updated
5.3 years ago by
Chris S. • 290
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5
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4.1k
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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 5.5 years ago by
Pavel Senin • 1.9k
0
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2
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3.9k
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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 5.6 years ago by
Pavel Senin • 1.9k
0
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2
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3.9k
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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 5.6 years ago by
Pavel Senin • 1.9k
Latest awards to Pavel Senin
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Is there a way to filter out files by a taxon and a tissue in SRAdb?
Scholar
20 months ago,
created an answer that has been accepted.
For A: Stress Response: is there a mapping between KEGG and COG? [solved]
Appreciated
2.1 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
2.1 years 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
2.4 years ago,
created an answer that was upvoted at least 5 times.
For A: Superimpose 2 Heatmaps
Popular Question
2.6 years 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
2.6 years ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Snp Format For Gff3: 'Name=' Vs 'Id='
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For Stress Response: is there a mapping between KEGG and COG? [solved]
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For Snp Format For Gff3: 'Name=' Vs 'Id='
Appreciated
4.3 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question
4.6 years ago,
created a question with more than 1,000 views.
For Pauda (Bowtie) Exception While Processing Microbial_Refseq
Teacher
5.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Identify The Protein Domains Of A Specific Protein?
Commentator
5.2 years ago,
created a comment with at least 3 up-votes.
For C: Problem With Perl Script When Extracting Sequences According To The Ids
Appreciated
5.2 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Appreciated
5.6 years ago,
created a post with more than 5 votes.
For C: How to extract unique mapped reads from your bam files?
Scholar
5.6 years ago,
created an answer that has been accepted.
For A: Stress Response: is there a mapping between KEGG and COG? [solved]
Good Answer
5.8 years ago,
created an answer that was upvoted at least 5 times.
For A: How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frame
Appreciated
6.0 years ago,
created a post with more than 5 votes.
For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Commentator
6.1 years ago,
created a comment with at least 3 up-votes.
For C: Problem With Perl Script When Extracting Sequences According To The Ids
Scholar
6.1 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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