User: cpad0112

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Posts by cpad0112

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Comment: C: how to make a .tbi file of .gtf.gz?
... in addition, gtf =~ gff2 ...
written 12 hours ago by cpad01123.8k
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Comment: C: memory size error in R
... If you are huge number of CEL files and limited by RAM, I would suggest to use Aroma (https://www.aroma-project.org/) frame work. Instead of keeping in memory, it keeps writing to hard disk. As a result, it would take more HDD space. Since lots of IO is involved, analysis would be a little bit slow ...
written 1 day ago by cpad01123.8k
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Answer: A: How can I calculate coverage from the base frequencies file?
... try sequence logos. Below code is for %: cov <-read.csv("test.txt", header = T, sep="\t", stringsAsFactors = F) df=data.frame(cov[1], percentage=(apply(cov[,-1],1,sum)/sum(cov[-1]))*100) output: > df Position percentage 1 0 0.3558719 2 4 0.0000000 ...
written 2 days ago by cpad01123.8k
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Comment: C: pairwise comparison in R
... @OP: There was a similar post by you and you didn't resolve this: https://www.biostars.org/p/289256/#289288 and i am not sure if you need raw data in pairwise comparison. Run without raw data. pair<-pairwise.comparison(data.mas5, "celline", c("c.oh","5AzadC.48h")) Example code that works ...
written 2 days ago by cpad01123.8k
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Comment: C: R: Convert ShortReadQ class to DNAStringSet?
... Did you try your shortread object @sread? it is a dnastringset object. From manual, shortreadQ class contains DNAStringSet, Quality, ShortReadQ objects with in it. `class(fq@sread), class(sread(fq))` should give you DNAstringset object (fq being "ShortReadQ" object) Example code: fl <- sys ...
written 2 days ago by cpad01123.8k
1
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Comment: C: How to identify and count multi-exon genes
... np. next time, please post example data. ...
written 2 days ago by cpad01123.8k
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Comment: C: awk one line command
... If original file name is "test.bed", and you want to append this to every chromosome file to be created, then command would be: $ seq 22 | parallel "grep -w chr{} test.bed > test.bed.chr{}.bed" This would create multiple files with original name and the chromosome name. ...
written 2 days ago by cpad01123.8k
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Comment: C: awk one line command
... That is correct. But it can be improved with -w option: $ seq 22 | parallel "grep -w chr{} test.bed > chr{}.bed" Example bed: $ cat test.bed chr1 10094 10144 563_280_1408 1 + chr1 10095 10144 421_286_567 0 + chr2 10165 10215 382_570_1514 9 + chr2 10170 10196 664_789_4 ...
written 2 days ago by cpad01123.8k
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Comment: C: How to identify and count multi-exon genes
... It is possible outside R. Btw, what is the cut off for multi exon genes. Following code is for genes with more than 1 exon. Example gtf: $ head ucsc.refgene.hg38.gtf chr1 refGene exon 11874 12227 . + . gene_id "DDX11L1"; transcript_id "NR_046018"; exon_number "1"; exon_id "NR_046018.1"; ...
written 3 days ago by cpad01123.8k
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Comment: C: SnpSift doesn't show any VariantType for filtering
... If you are looking for summary, then you look into summary.html from snpeff ...
written 3 days ago by cpad01123.8k

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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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