Moderator: cpad0112

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cpad011212k
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Posts by cpad0112

<prev • 1,930 results • page 1 of 193 • next >
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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 cpad011212k
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Comment: C: Is it necessary to trim adaptor sequences?
... 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 cpad011212k
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Comment: C: Add error bars to barplot that uses melted dataframe in R
... try geom_errorbar https://www.biostars.org/u/58421/ ...
written 7 days ago by cpad011212k
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Comment: C: calculate the average of column 7 if the rows of column 2 have the same value
... 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 cpad011212k
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... @ 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 cpad011212k
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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 cpad011212k
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... 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 cpad011212k
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Comment: C: Extract Transcript sequence from fastq file (Plant RNA-Seq data)
... 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 cpad011212k
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Comment: C: Extract Transcript sequence from fastq file (Plant RNA-Seq data)
... @ 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 cpad011212k
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Comment: C: calculate the average of column 7 if the rows of column 2 have the same value
... 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 cpad011212k

Latest awards to cpad0112

Scholar 1 day ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Scholar 12 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 20 days ago, created an answer that has been accepted. For A: which feature is considered as expression level ?
Scholar 20 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 3 months ago, created an answer that has been accepted. For A: which feature is considered as expression level ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Appreciated 5 months ago, created a post with more than 5 votes. For C: Remove columns and rows which have only NAs without deleting all the data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 6 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change

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