Moderator: cpad0112
cpad0112 ♦ 12k
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Posts by cpad0112
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Comment:
C: Greedy-Non greedy Pattern search
... please read about ternary operators and zero length assertions.@ https://www.biostars.org/u/48122/ ...
written 4 hours ago by
cpad0112 ♦ 12k
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... https://www.biostars.org/p/212136/
https://biostar.usegalaxy.org/p/26923/
http://seqanswers.com/forums/showthread.php?t=71558 ...
written 6 days ago by
cpad0112 ♦ 12k
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... try geom_errorbar https://www.biostars.org/u/58421/ ...
written 7 days ago by
cpad0112 ♦ 12k
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... I am not sure what is going on. Probably it is not sorted proper. Could you please post a few records at the place record jumping (for eg 10 records that side and 10 records this side with identical 2nd column values)? @ https://www.biostars.org/u/42729/
if sorting is the issue, try this with [tsv- ...
written 7 days ago by
cpad0112 ♦ 12k
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... @ https://www.biostars.org/u/51062/
I guess you forgot to use parallel. Try installing parallel and use the below function:
parallel 'seqkit range -r {}:{} *.fasta -o output/group_{}.fasta' ::: $(seq 1 $(grep -c ">" species1.fasta)) ...
written 8 days ago by
cpad0112 ♦ 12k
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Comment:
C: problem installing prokka
... check the permissions of : /home/paulo/anaconda3/lib/site_perl/5.26.2/Algorithm ...
written 9 days ago by
cpad0112 ♦ 12k
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... 1. make a directory "output" in the same directory where all fasta files are located.
2. run following command:
$ parallel seqkit range -r {}:{} *.fasta -o output/group_{}.fasta ::: $(seq 1 $(grep -c ">" species1.fasta))
**do not output fasta files in the same directory**. Download seqk ...
written 9 days ago by
cpad0112 ♦ 12k
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... I guess Trinity is for *de novo* assembly. Since reference genome and annotation are available, use reference based assembly. Authors in this paper (on *B. napus* transcriptome) https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2062-7 used tophat. I would suggest hisat2 or star. You ...
written 9 days ago by
cpad0112 ♦ 12k
1
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... @ https://www.biostars.org/u/21757/
Is this plant genome already sequenced and annotated? If so, go for reference based assembly (with reference sequence) and post alignment, you can extract transcripts (sequence) of interest using annotation file. For aligning RNAseq data, use splice aware aligner ...
written 9 days ago by
cpad0112 ♦ 12k
1
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... with [datamash][1]:
$ datamash -sH -g 2 mean 7 < test.txt | sort -k 1n
GroupBy(wind_start) mean(relative_t_o)
1 1
10001 1
40001 1
110001 1
140001 0.956521739
[1]: https://www.gnu.org/software/datamash/
...
written 9 days ago by
cpad0112 ♦ 12k
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For C: Problem installing Rgraphviz in R
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