User: cpad0112

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Posts by cpad0112

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Comment: C: Authorship conflict and resolution
... **IMO**, keep him as co author and provide correct address of correspondence to the journal.Before you proceed, 1) Inform him of manuscript submission date, send him a draft for correction and ask him if manuscript needs any changes. Keep a copy of communication. 2) keep all other communications w ...
written 23 hours ago by cpad01122.3k
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Comment: C: Indel detectors for Ion Torrent data
... 1. Was there a recalibration step with known indels post alignment? 2. You can also try PINDEL derivatives like DINDEL, GINDEL etc. DINDEL takes output from PINDEL. ...
written 1 day ago by cpad01122.3k
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Answer: A: Delete ID only if not presnt in next line (lines are in pair)
... $ awk -F: '{split($2,a,",");for(i in a)print $1"\t"a[i]}' test | sort -k2 | uniq -D -f1 | sed 's/\t/:/g' rsid1:sample1 rsid2:sample1 rsid3:sample6 rsid4:sample6 input (test): rsid1:sample1,sample2,sample3 rsid2:sample1,sample5 rsid3:sample4,sample6 r ...
written 2 days ago by cpad01122.3k
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Answer: C: Compare between two columns of two different files and print common
... Another working solution in awk: $ awk 'FNR==NR{a[$5]++;next}a[$6]' test1.txt test2.txt Chr1 NC_029516.1 5341 19961 - LRRC16B Chr1 NC_029516.1 20428 23408 - LOC107314597 Chr1 NC_029516.1 23722 31174 + LOC107305688 ...
written 4 days ago by cpad01122.3k
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Comment: C: SNP associated disease
... try also clinical browser (https://www.ebi.ac.uk/eva/?Clinical%20Browser) ...
written 5 days ago by cpad01122.3k
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Answer: A: How to match and merge two tables in a effective way where sample names are same
... test1 and test2 are copy/pasted from OP. R code below merges both the files (loaded from . csv) and row values are added (sum). In R: test1=read.csv("test1.csv", header = T, sep = ",", stringsAsFactors = F) test2=read.csv("test2.csv", header = T, sep = ",", stringsAsFactors = F) test1 ...
written 6 days ago by cpad01122.3k
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Comment: C: Statistics graduate wants to do some bioinformatics analysis
... I guess you are living in a bubble. In bioinformatics industry, most of the bioinformatics project do not even have SME in biology. Look at the requirements of most of the bioinformatics jobs or interview questions.Most of these positions require programmers /developers with or without biology knowl ...
written 6 days ago by cpad01122.3k
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Comment: C: Explain fig. 5 c of "The impact of rare variation on gene expression across tiss
... - Figure a is self explanatory. It is RIVER model - Figure b is comparative predictive power between two methods: RIVER (integrates genomic and transcriptomic information) and another method using genomic annotations only. My understanding is that gene expression is being predicted. ...
written 6 days ago by cpad01122.3k
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Comment: C: Statistics graduate wants to do some bioinformatics analysis
... IMO, there is not much biology in bioinformatics. Try to pick up programming skills (java, python, perl, awk, sed..not in any order or not in any preference, for those who are offended by the list) and some database (mysql, oracle, post gresql) skills. In addition pick up some high throughput compu ...
written 6 days ago by cpad01122.3k
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Comment: C: Explain fig. 5 c of "The impact of rare variation on gene expression across tiss
... Pathogenic SNVs annotated in ClinVar are shown in: - red if they were likely regulatory (nonsense, splice site, or synonymous) - orange otherwise (missense) ...
written 6 days ago by cpad01122.3k

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Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Scholar 5 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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