User: mkulecka

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mkulecka320
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European Union
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1 week ago
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5 years, 3 months ago
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Posts by mkulecka

<prev • 56 results • page 1 of 6 • next >
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Comment: C: GSEA using clusterProfiler
... Maybe you have your IDs as numbers - clusterProfiler expects them to be characters. ...
written 19 months ago by mkulecka320
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Comment: C: Error in SAMseq analysis with R
... I am experiencing the same problem. Any resolution for that? ...
written 2.1 years ago by mkulecka320
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Answer: A: Identifying CNVs from targeted amplicon sequencing
... I have used CONTRA (https://www.ncbi.nlm.nih.gov/pubmed/22474122). This software is supposedly tuned for targeted sequencing. ...
written 2.5 years ago by mkulecka320
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Answer: A: Can I determine the machine used for RNA-seq from the .count file extension?
... Don't you have a bam file with alignments? If you're lucky, the platform info should be in read group (@RG) section of header, under PL or PM tag (as per SAM format specification - https://samtools.github.io/hts-specs/SAMv1.pdf). ...
written 2.5 years ago by mkulecka320
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Answer: A: Way too much data generated for 1 WGS sample
... Maybe you should try combination of approaches 1 and 3 - allign reads to the reference and then subsample the bam file (for example with samtools view -s option). ...
written 2.7 years ago by mkulecka320
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Comment: C: Pca From Vcf Files
... With R it's pretty easy: library(ggplot2) library("ggrepel") df<-read.delim("plink.eigenvec") #read in eigenvectors eigens<-read.delim("plink.eigenval",header=F) #read in eignevalues sum_eig<-sum(eigens$V1) sum_eigs<-lapply(eigens$V1,function(x){ rt<-(x/sum_eig)*100 rt<-r ...
written 2.7 years ago by mkulecka320
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Comment: C: Merge multiple vcf files while preserving FILTER information
... Unfortunately it doesn't preserve information on all filters - it can mark variant only as PASS or FAILED but not both, if ti passes a filter in one sample but not the other. ...
written 3.0 years ago by mkulecka320
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Merge multiple vcf files while preserving FILTER information
... Hello, I have multiple vcf files from different samples. I would like to combine all of the in one file but I would like to preserve information from FILTER field. For example if I have a vcf record which passes the filter in one sample: > chr1 949654 . A G 571.55 PASS and fails it another > ...
vcf merge variants written 3.0 years ago by mkulecka320 • updated 3.0 years ago by _r_am31k
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Long non-coding RNA database in mouse
... Hello everyone, Does anyone know any good tool for functional annotation of long non-coding RNAs in mice? I'm interested in getting information on about 165 lncRNAs so a database with some sort of programmatic access would be ideal. I know of [lncRNAdb][1] , but maybe someone can recommend other op ...
rna-seq lncrna written 3.8 years ago by mkulecka320 • updated 3.8 years ago by Biostar ♦♦ 20
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Comment: C: usearch version, which one use to get results faster?
... I don't know much about technical aspects of computers but I think 64bit programmes can use more memory than 32bit ones. The limit for 32bit is 4GB - if you have more RAM than that, you should benefit from 64bit version. ...
written 4.0 years ago by mkulecka320

Latest awards to mkulecka

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: RNA-Seq Analysis: To sort or not to Sort?
Popular Question 11 months ago, created a question with more than 1,000 views. For Finding the largest possible combination of mutations
Scholar 12 months ago, created an answer that has been accepted. For A: Notable open source bioinformatics projects written in Java?
Popular Question 15 months ago, created a question with more than 1,000 views. For Long non-coding RNA database in mouse
Popular Question 15 months ago, created a question with more than 1,000 views. For Merge multiple vcf files while preserving FILTER information
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Ion Torrent Proton RNASeq reads alignment
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Check whether a fasta header has sequence underneath it
Scholar 4.8 years ago, created an answer that has been accepted. For A: Check whether a fasta header has sequence underneath it
Supporter 4.9 years ago, voted at least 25 times.
Scholar 5.0 years ago, created an answer that has been accepted. For A: Check whether a fasta header has sequence underneath it
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Check whether a fasta header has sequence underneath it

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