User: Pavel Senin

gravatar for Pavel Senin
Pavel Senin1.8k
Reputation:
1,820
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Location:
Los Alamos, NM
Website:
http://seninp.github.io/
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Google Scholar Page
Last seen:
2 months ago
Joined:
5 years, 2 months ago
Email:
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i like doughnuts 

Posts by Pavel Senin

<prev • 256 results • page 1 of 26 • next >
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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 2.5 years ago by Pavel Senin1.8k
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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 ...
written 2.5 years ago by Pavel Senin1.8k
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Comment: C: Is there a way to filter out files by a taxon and a tissue in SRAdb?
... 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. ...
written 2.9 years ago by Pavel Senin1.8k
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Is there a way to filter out files by a taxon and a tissue in SRAdb?
... 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! ...
sradb written 2.9 years ago by Pavel Senin1.8k • updated 2.8 years ago by Lynxoid210
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Comment: C: Is there a way to know sequences length when querying ENA programmatically?
... also accepted. XML is a better way to get data, parsing/debugging it is the pain though. ...
written 2.9 years ago by Pavel Senin1.8k
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Comment: C: Is there a way to know sequences length when querying ENA programmatically?
... That works, but you also need to divide by 2 for paired-end libraries :)! ...
written 2.9 years ago by Pavel Senin1.8k
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Is there a way to know sequences length when querying ENA programmatically?
... 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 ...
rna-seq ena written 2.9 years ago by Pavel Senin1.8k • updated 2.9 years ago by Chris S.270
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Comment: C: Pathway analysis for transcriptome profiles
... This article may help you. It has a table of tools and approaches. I am not affiliated with these guys.  ...
written 3.1 years ago by Pavel Senin1.8k
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Comment: C: How to calculate sum of branch lengths between specified leaves from a Newick tr
... 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 3.1 years ago by Pavel Senin1.8k
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Answer: A: How to calculate sum of branch lengths between specified leaves from a Newick tr
... 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 3.1 years ago by Pavel Senin1.8k

Latest awards to Pavel Senin

Popular Question 9 months ago, created a question with more than 1,000 views. For Snp Format For Gff3: 'Name=' Vs 'Id='
Popular Question 9 months ago, created a question with more than 1,000 views. For Stress Response: is there a mapping between KEGG and COG? [solved]
Appreciated 14 months ago, created a post with more than 5 votes. For C: How to extract unique mapped reads from your bam files?
Popular Question 19 months ago, created a question with more than 1,000 views. For Snp Format For Gff3: 'Name=' Vs 'Id='
Appreciated 22 months ago, created a post with more than 5 votes. For C: How to extract unique mapped reads from your bam files?
Popular Question 23 months ago, created a question with more than 1,000 views. For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Rsamtools & Iranges, Getting Junction-Aware Coverage
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Pauda (Bowtie) Exception While Processing Microbial_Refseq
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How To Identify The Protein Domains Of A Specific Protein?
Commentator 2.7 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 2.8 years ago, created a post with more than 5 votes. For C: How to extract unique mapped reads from your bam files?
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: How to extract unique mapped reads from your bam files?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Stress Response: is there a mapping between KEGG and COG? [solved]
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Superimpose 2 Heatmaps
Good Answer 3.4 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 3.6 years ago, created a post with more than 5 votes. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Commentator 3.6 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 3.6 years ago, created an answer that has been accepted. For A: Stress Response: is there a mapping between KEGG and COG? [solved]
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Why Perl Or Sed Command Not Working
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Bwa Mem Have Different Alignment Result When Using Different Threads
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Why Perl Or Sed Command Not Working
Guru 3.9 years ago, received more than 100 upvotes.
Centurion 3.9 years ago, created 100 posts.

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