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Moderator: h.mon

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h.mon ♦ 3.9k
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Posts by h.mon

<prev • 677 results • page 1 of 68 • next >
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Comment: C: Problem with SMART
... Did you `hmmpress` you HMM profile? **edit**: in general, you should provide more details, such as command used, which HMM profile, and so forth. ...
written 4 days ago by h.mon ♦ 3.9k
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Answer: A: How to use de novo assembly to build onto an existing reference-guided assembly.
... You could try [MITObom][1] or [Arc][2], using your drafts as starting points. [1]: https://github.com/chrishah/MITObim [2]: https://ibest.github.io/ARC/ ...
written 9 days ago by h.mon ♦ 3.9k
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Comment: C: how to get transcript annotation in GTF format
... Read ["Tutorial: How To Ask Good Questions On Technical And Scientific Forums"][1], and then elaborate a bit more your question. [1]: https://www.biostars.org/p/75548/ ...
written 11 days ago by h.mon ♦ 3.9k
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Comment: C: inversion detection in sequencing
... You probably mean Lumpy? Or is there a Lumy as well? ...
written 15 days ago by h.mon ♦ 3.9k
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Answer: A: Is it necessary to name sort single end reads before htseq count
... It should not make any difference for single-end data, but you can easily test: just run htseq-count with both options, one at a time. The `--pos` argument is used to determine how paired reads are sorted on the sam/bam file, to select internally how to find read pairs. ...
written 15 days ago by h.mon ♦ 3.9k
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Comment: C: All reads with mapq value <= 1, htseq does not attribute counts to any feature
... What was your previous bowtie2 command? The command you posted seems pretty standard, I wonder what you were trying before. ...
written 15 days ago by h.mon ♦ 3.9k
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Comment: C: align two long sequences using Muscle but found gaps only
... Basically, you are using the wrong tool for the task you want. Try Mauve, BWA (not sure if it handles 40K long sequences, though) or even Blast. **edit**: also, see [this][1] thread. [1]: https://www.biostars.org/p/67632/ ...
written 15 days ago by h.mon ♦ 3.9k
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Comment: C: All reads with mapq value <= 1, htseq does not attribute counts to any feature
... I assume you have RNAseq data? Check [this][1] answer, and do the same: use BBDuk to check for rRNA contamination on your samples. You may also use SortMeRNA for this, I think it is slightly more sensitive, but a lot slower. Either way, you will know how bad your rRNA contamination was, and both pro ...
written 16 days ago by h.mon ♦ 3.9k
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Comment: C: Denovo assembly of Putative Plasmid
... My only suggestion at this point is for you to type all the command from the beginning (do not copy / paste), and use tab completion where appropriate to avoid errors. ...
written 16 days ago by h.mon ♦ 3.9k
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Comment: C: How can I compare my CLC denovo variants against BWA+samtools variants?
... Did you apply any quality filters to avoid spurious SNPs? And please, update your question, describing what you did in more detail. ...
written 17 days ago by h.mon ♦ 3.9k

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Commentator 25 days ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Scholar 3 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 3 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
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Appreciated 4 months ago, created a post with more than 5 votes. For A: RNAseq design: differential expression between sexes in several species
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Student 4 months ago, asked a question with at least 3 up-votes. For Benchmarking bioinformatics tools
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Commentator 4 months ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 4 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 4 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 5 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: FastQC Error Problem
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 5 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 5 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 5 months ago, created a post with more than 5 votes. For A: RNAseq design: differential expression between sexes in several species
Scholar 5 months ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
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