Moderator: lieven.sterck

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lieven.sterck6.3k
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Posts by lieven.sterck

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Comment: C: readTranscriptFeatures from genomation
... A small educational note: I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: ![101010 Button][1] [1]: https://i.ibb.co/3rQtWPB/formatbar ...
written 17 hours ago by lieven.sterck6.3k
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Answer: A: Want read count with respect to geneID instead of transcript IDs
... Have a look in the manual of [htseq-count][1] and pay especially attention to the `-t` and `-f` parameters. Then look in your GFF file and choose the feature tags that correspond to your question and use those when running htseq-count [1]: https://htseq.readthedocs.io/en/release_0.11.1/count.ht ...
written 19 hours ago by lieven.sterck6.3k
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Comment: C: MUMmer . Global alignment
... Please go through https://www.biostars.org/p/357878/ and then consider editing your question. it always good to give us some info on what you are trying to do exactly. what command lines did you ran? things like that ...
written 1 day ago by lieven.sterck6.3k
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Comment: C: MUMmer . Global alignment
... Tool requests are `Question` posts, not `Tool` posts (the latter are for announcements of new software etc). I’ve changed it for you this time, but please bear it in mind for the future. ...
written 1 day ago by lieven.sterck6.3k
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Comment: C: I use update_blastdb.pl to update nr database, and problem come out
... did you have a look at what it tries to do at the lines it reports (in the update_blastdb.pl script)? ...
written 1 day ago by lieven.sterck6.3k
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Comment: C: which scoring matrix to use in shore (shoremap) analysis
... thanks for the insights https://www.biostars.org/u/6093/ , very useful ! I was under the impression that since my genome is homozygous I should go for the `_hom` one . but you seem to indicate differently (and making more sense likely) but could you elaborate a little how you come to that conclusio ...
written 6 days ago by lieven.sterck6.3k
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which scoring matrix to use in shore (shoremap) analysis
... I recently started to work with `shore` and `shoremap` (mainly because my collaborators requested so) in order to pinpoint ems mutations in an Arabidopsis line they created. While the majority of the protocol runs successful , I'm in doubt about which scoring matrix to use in the `shore consensus` ...
matrix shore shoremap written 7 days ago by lieven.sterck6.3k
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Comment: C: index genome using haploid genome.fa or diploid genome.fa?
... Unless specifically done so, even diploid genomes are usually assembled in a haploid state. What species are we talking about here and do you have any insights in how it was assembled? ...
written 8 days ago by lieven.sterck6.3k
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Comment: C: Help with awk command
... that is strange indeed. With me it does print all entries to the output file. Your output looks more like what you would get with this command: for file in `cat Samples.txt`; do echo $file > TestFile.txt ; done If your script is a loop in loop kinda system, can you check you did not put th ...
written 11 days ago by lieven.sterck6.3k
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Comment: C: Help with awk command
... what does: for file in `cat Samples.txt`; do echo $file; done give as output? ...
written 11 days ago by lieven.sterck6.3k

Latest awards to lieven.sterck

Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 10 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 10 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 11 weeks ago, created an answer that has been accepted. For A: List of all GO terms
Scholar 4 months ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Delete numbers in the tables column
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Appreciated 5 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Scholar 5 months ago, created an answer that has been accepted. For A: List of all GO terms
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Rename FASTA files according to FASTA file header
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Gene Prediction Softwares
Scholar 6 months ago, created an answer that has been accepted. For A: List of all GO terms

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