User: Francesco

gravatar for Francesco
Francesco10
Reputation:
10
Status:
New User
Location:
Erasmus MC (NL)
Last seen:
6 days, 18 hours ago
Joined:
10 months ago
Email:
f*********@gmail.com

Posts by Francesco

<prev • 7 results • page 1 of 1 • next >
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Pooling WT and CRISPR/Cas9 KOs cells in the same scRNAseq sample and then demultiplex by puromycin resistance cassette expression
... Library preparation for single cells RNA sequencing ends being the most expensive part of the of the process, so **it's way cheaper doubling the reads depth than the number of samples.** I have seed already somebody pooling mouse and human cells in the same sample and then demultiplex the cells by u ...
crispr-cas9 scrnaseq rna-seq written 4 months ago by Francesco10 • updated 3 months ago by jockbanan390
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RNAseq variant calling: STAR align promotes mismatched overhanging mappings onto introns instead of calling splicing junctions
... Hi, I'm doing **variant calling from my RNAseq** data on a cell line (Paired End 2X100b, Illumina) I'm following GATK workflows and everything is working almost fine since I can find all the expected mutations already characterized in my cell line. The problem is that I see some additional mutations ...
splicing junction star rna-seq written 4 months ago by Francesco10
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Answer: C: Error running cutadapt in multithread mode
... Thank you, I created a conda enviroment for cutadapt with python 3.7 and now it's working in multicore. Thank you so much! ...
written 5 months ago by Francesco10
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Error running cutadapt in multithread mode [SOLVED]
... I'm running cutadapt on MacOS Catalina 15.10.6: This is cutadapt 2.10 with Python 3.8.3 I have pigz installed and the script is working perfetly in single core. I also tried specifying to use just 2 cores but I get the same error. I also tried to execute the trimming of the adapter in single ...
adapter trimming rna-seq cutadapt written 5 months ago by Francesco10
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Answer: A: ExomeDepth error in getBamCounts when adding a fasta reference
... **Solved!** It's very likely it was an overflow problem that R encounters with files bigger than 2GBs (as the hg19 fasta file) I manually computed the GC content of all the exonic regions with bedtools: $ bedtools nuc -fi hg19.fa -bed S07604514_hs_hg19/S07604514_Covered_edit.bed | awk '{$4=""; ...
written 9 months ago by Francesco10
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ExomeDepth error in getBamCounts when adding a fasta reference
... Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function: my.countsV6 <- getBamCounts(bed.frame =AgilentV6, bam.files = BAMFiles, include.chr = TRUE, ...
exomedepth cnv R written 9 months ago by Francesco10
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Forum: make sense out of Whole Exome Sequencing on cancer cell lines
... Hi, I'm Francesco, this is my first post on your nice forum so I suppose I should introduce myself. I'm a young MD with strong interest in base research and I'm trying to move into the world of bioinformatic. I hope you can give me some insights on the right direction to pursue and on some bioinform ...
sequencing forum next-gen snp whole exome sequencing written 10 months ago by Francesco10

Latest awards to Francesco

Scholar 5 months ago, created an answer that has been accepted. For A: ExomeDepth error in getBamCounts when adding a fasta reference
Scholar 9 months ago, created an answer that has been accepted. For A: ExomeDepth error in getBamCounts when adding a fasta reference

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