User: bow

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bow790
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790
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Netherlands
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http://bow.web.id
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3 years, 6 months ago
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7 years, 1 month ago
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Posts by bow

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Comment: C: Biopython SearchIO HMMer 3 parsing, HMM model length?
... Hi Jon, Indeed that's the correct solution. You can only get the hit's length (HMM in this case) when using the domain table format. It should have been clearer in the documentation, I admit. I've just updated the documentation so future versions should have this corrected.   Thanks for posting th ...
written 3.5 years ago by bow790
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Answer: A: Can't access individual attributes of tabular outfmt 6 blast output while parsin
... I see some of the questions have been addressed in the comments, so I will respond to some that have not (paraphrased): > 1. How can I access the qlen and slen attributes ? Since `qlen` is a property of the whole query, accessing it can be done via `blast_qresults.seq_len` in your case. Similar ...
written 4.6 years ago by bow790
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Comment: C: Can't access individual attributes of tabular outfmt 6 blast output while parsin
... The output file seems to contain 14 columns, though. @Bara'a, could you paste the command you used to get this results? If you did indeed specify two extra columns (qlen and slen), then I think your `fields` argument is correct. ...
written 4.6 years ago by bow790
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Comment: C: BigWig library for Java
... Hmm..the TDF format is usable only within IGV it seems? And yes, I am aware of other ways to create BigWig files from BAM files. This is actually the way we are doing this now in-house. But we're trying to reduce external dependencies (that step, for example, requires 2 executables and 1 extra data ...
written 4.6 years ago by bow790
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Comment: C: BigWig library for Java
... I need to share data with other people and sometimes load them into the track browser myself. BAM files are not that suitable because wading through multiple BAM files in IGV slows it down quite a lot. This is not the case with BigWig files. It's also easier and more compact to share BigWig files gi ...
written 4.6 years ago by bow790
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Comment: C: BigWig library for Java
... Not wig and bed per se, but yes, I do need them. Unless there is a similar (or better) format that allows me to view tracks without uploading them to the track browser.. ...
written 4.6 years ago by bow790
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BigWig library for Java
... Does anybody have recommended Java or Scala library for writing BigWig / BedGraph files? I am aware that there is a Java bigwig library that was developed by the IGV team. However, it seems to only provide BigWig / BedGraph reading functions; nothing on writing. After contacting the developers I wa ...
bedgraph java bigwig written 4.6 years ago by bow790 • updated 8 months ago by holgerbrandl30
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Comment: C: Comparing FPKM values from cufflinks and cuffnorm
... Indeed. Though when plotting the results against each other, depending on whether I use bias correction or not on Cufflinks, I could get either a linear scaling down or not. If I use the `-u` and `-b` flag on Cufflinks, Cuffnorm seems to only normalize linearly. This is not the case when I don't use ...
written 4.8 years ago by bow790
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Comparing FPKM values from cufflinks and cuffnorm
... I am trying to calculate an expression value that are comparable in one sample (so I can compare gene A, gene B, etc in the same sample) and across samples (so I can compare gene A in sample 1 with gene A in sample 2, and so on). My samples are from single-cell RNA sequencing and I've been using the ...
cufflinks cuffnorm rna-seq sequencing written 4.8 years ago by bow790 • updated 4.8 years ago by Biostar ♦♦ 20
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Comment: C: Fastqc Shows A Weird Kmer Distribution
... How did you remove the TruSeq-containing sequences? ...
written 5.9 years ago by bow790

Latest awards to bow

Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Getting Untranslated Dna Subject String As Output From Tblastn Via Biopython
Student 4.2 years ago, asked a question with at least 3 up-votes. For Comparing FPKM values from cufflinks and cuffnorm
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Comprehensive Intro To Next Generation Sequencing
Scholar 4.6 years ago, created an answer that has been accepted. For A: Can't access individual attributes of tabular outfmt 6 blast output while parsin
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Getting Untranslated Dna Subject String As Output From Tblastn Via Biopython
Great Question 4.6 years ago, created a question with more than 5,000 views. For How Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Biopython Seqio - Why Is It Repeating Deflines?
Appreciated 5.8 years ago, created a post with more than 5 votes. For Comprehensive Intro To Next Generation Sequencing
Good Question 5.8 years ago, asked a question that was upvoted at least 5 times. For How Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
Good Question 5.8 years ago, asked a question that was upvoted at least 5 times. For Comprehensive Intro To Next Generation Sequencing
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Biopython Seqio - Why Is It Repeating Deflines?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For How Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Reading Ab1 Files With Python
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Comprehensive Intro To Next Generation Sequencing
Popular Question 5.8 years ago, created a question with more than 1,000 views. For How To Interpret/Reconcile The Counts Obtained Via Samtools Flagstat
Supporter 5.8 years ago, voted at least 25 times.
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Getting Untranslated Dna Subject String As Output From Tblastn Via Biopython
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Biopython Seqio - Why Is It Repeating Deflines?
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Running Blastp From Biopython And Only Looking For Exact Matches
Student 5.8 years ago, asked a question with at least 3 up-votes. For How Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
Student 5.8 years ago, asked a question with at least 3 up-votes. For Reading Ab1 Files With Python
Student 5.8 years ago, asked a question with at least 3 up-votes. For Comprehensive Intro To Next Generation Sequencing

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