oma Posts

A: How do you extract longest transcript from fasta file using length and header ID by JC ♦ 8.7k
The commands are complex to control, imho it's better if you put that logic in a script: #!/...
C: normalization in cross meta-analysis by JC ♦ 8.7k
1. Normalization is before merge at probeset level https://www.biorxiv.org/content/biorxiv/early/...
C: Summing up prob level by Kevin Blighe ♦ 49k
That is correct.
C: non-SNP variants in a vcf merge file by Kevin Blighe ♦ 49k
Please let me know if it works....
A: how to merge the DNA_methylation data downloaded for GDC database by Kevin Blighe ♦ 49k
ChAMP does not necessarily have to read iDAT files. Please check the vignette and documentation f...
C: How to make a loop to run kallisto bus command for so many fastq.gz files at onc by archana.bioinfo87 • 170
You can also make two directory for R1 and R2 mkdir R1 mkdir R2 mv *R1_001.fastq.gz ...
C: gvcf error bcftools by Kevin Blighe ♦ 49k
It is likely just failing some filter, which may or may not be related to read depth. Can you sca...
C: download from SRA by MSF • 0
As I wrote in my comment "From what I read", as I was reading there already :).To me, it does not...
C: Reference / Gold-standard FASTQ file for NGS pipeline comparison ? by Kevin Blighe ♦ 49k
As per my colleague, genomax, GIAB (Genome in a Bottle) is the standard that most people use for ...
C: non-SNP variants in a vcf merge file by evelyn • 30
Thank you, @Kevin! I will try this.
A: non-SNP variants in a vcf merge file by Kevin Blighe ♦ 49k
Some variant callers just call variants in this way. You can probably mitigate these by 'normalis...
A: MAF threshold in The Cancer Genome Atlas (TCGA) and Personal Genome Project (PGP by Kevin Blighe ♦ 49k
For PGP, please inquire direct to the UK team at UCL: https://www.personalgenomes.org.uk/ For t...

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