User: microfuge

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microfuge1.1k
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Posts by microfuge

<prev • 205 results • page 1 of 21 • next >
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Comment: C: How to install SortMeRNA tool on my university HPC cluster?
... Also there seems to a direct binary available http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-2.1-linux-64-multithread.tar.gz I have not used it but I could extract and just a `./sortmerna` seems to work. ...
written 17 days ago by microfuge1.1k
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Comment: C: How Do I create a BED file from an hard masked fasta?
... the `twoBitInfo` command from kentUtils (available here http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) has an option `-nBed` to get a bed file of N stretches. You will need to convert the fasta to twobit by another command `twoBitToFa` also available at the same site. ...
written 19 days ago by microfuge1.1k
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Comment: C: How do I find the same gene in two different assemblies?
... For non coding genes, UTRs etc it would also be good to generate a chain file for liftOver (provided only assemblies are different and species are same/very_similar) . I have used this pipe line https://github.com/wurmlab/flo with good results to generate chain files which then can be used by crossm ...
written 28 days ago by microfuge1.1k
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Comment: C: Testing uniform distribution of SNPs across chromosome
... At this stage I would suggest to upvote/accept_as_answer the detailed comments by @i.sudbery which nicely explain the concepts behind. ...
written 4 weeks ago by microfuge1.1k
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Comment: C: Testing uniform distribution of SNPs across chromosome
... I guess Poisson distribution makes more sense here and in that case distance between 2 adjacent SNPs should be gamma distributed. ...
written 5 weeks ago by microfuge1.1k
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Comment: C: repeatmasker empty output
... ok. You can check if your installed repeat libraries contain different types of TEs with the script that comes with repeatmasker. `queryRepeatDatabase.pl -species human -stat` This should dump different TE types (LINE, SINE ... ) . If the output does not contain these TE types then the output yo ...
written 7 weeks ago by microfuge1.1k
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Comment: C: repeatmasker empty output
... Thanks and sorry that I don't have a direct answer. What we do is use RepeatModeler http://www.repeatmasker.org/RepeatModeler/ . Then use the `queryRepeatDatabase.pl` which comes with RepeatMasker to dump the repeats in the species we use (eg `-species Carnivora` . The combine the repeatlibs g ...
written 7 weeks ago by microfuge1.1k
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Comment: C: repeatmasker empty output
... I think the TE type info is taken from fasta header of the repeat library `>SINEC2A2_CF#SINE/tRNA RepbaseID: SINEC2A2_CFXX ` Can you check if fasta header of your repeat library look like this ? ...
written 7 weeks ago by microfuge1.1k
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Comment: C: retrieve relative position of CDS start for every isoforme
... One approach could be to convert the gtf to bed12 and then the blockStart (exonstarts) are relative to chromStart (transcription start) so directly gives the distance needed (provided strand information is properly taken care of). ...
written 8 weeks ago by microfuge1.1k
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Answer: C: Split comma seperated list of GO terms into multiple rows and maintain gene iden
... My Apologies for the mistake Can you please try this - `cat your_input_file |perl -ane '{print map {$F[0]."\t".$_."\n" } split (/,/,$F[1]) }' ` ...
written 9 weeks ago by microfuge1.1k

Latest awards to microfuge

Scholar 3 months ago, created an answer that has been accepted. For C: BedTools getfasta -split
Guru 3 months ago, received more than 100 upvotes.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 12 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 12 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 12 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 13 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Popular Question 17 months ago, created a question with more than 1,000 views. For Tissue Specificity index (tau) should FPKM data be log transformed?
Scholar 22 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Scholar 23 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Scholar 23 months ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: chain file for maize
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Supporter 2.7 years ago, voted at least 25 times.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: chain file for maize
Centurion 2.7 years ago, created 100 posts.
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: Fasta alignment to Tajima's D and population statistics
Scholar 2.8 years ago, created an answer that has been accepted. For A: Many SRR files for one experiment. What are the steps to be taken before further

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