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Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
Comment: bcl-convert cannot create output directory structure at the path specified
C: why GATK makes things more complicated ?
Answer: RNA-Seq analysis
Comment: UMI-Tools knee-method has great influence on the results of white list
Answer: RNA-Seq analysis
Answer: salmon with long read
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Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
ATpoint
82k
> I would prefer to get the sample names from a sample sheet rather than parsing the library names with some dodgy regex. +1 !!!
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
MolGeek
▴ 50
You are right, thats a quick and dirty answer to get the means.
Comment: bcl-convert cannot create output directory structure at the path specified
by
GenoMax
142k
Looks like you are not using a samplesheet. You will have to use a samplesheet though if you want to create fastq files for index reads si…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
ATpoint
82k
Works here, but it's not generic or tidy since you have to manually enter the correct numbers and enter the colnames of the output.
Comment: Filtering reads that map to both references
by
Pierre Lindenbaum
162k
> I'm working in a micromamba environment. I've got jvarkit installed Hi , sorry I didn't write that jvarkit conda /env. i usually call jv…
Answer: Constructing single sequence genome assembly out of short reads
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Philipp Bayer
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It's very unlikely. The assembler did the best it could with the short data you have; any gaps that remain cannot be filled using short rea…
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
MolGeek
▴ 50
Or just use rowMeans and provide the desired columns (for dataframes with low number of columns): ```R p767.m <- data.frame(p767.AM = r…
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Hello Varsha, can you please clarify your question ? On what criteria do you want to subset the transcripts ?
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
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GenoMax
142k
https://www.biostars.org/u/110878/ : Please accept this answer (green check mark) to provide closure to this thread.
Comment: bcl-convert cannot create output directory structure at the path specified
by
giulia.trauzzi
▴ 10
Thanks! I am sure there are. Are these necessary to demultiplex the data though? I am assuming most demultiplexing tools do not require the…
Comment: Filtering reads that map to both references
by
GenoMax
142k
You can use `bbsplit.sh` from BBMap suite to map reads to multiple references and bin them accordingly. Take a look at the in-line help (`a…
Comment: bcl-convert cannot create output directory structure at the path specified
by
GenoMax
142k
Is that the only error? Can you provide the entire command line you are using? > as a customer is interested in getting the fastq files f…
Comment: Filtering reads that map to both references
by
michael.flower.14
▴ 180
Thanks Pierre. I'm working in a micromamba environment. I've got `jvarkit` installed. I updated your filter script as follows. # Creat…
Comment: bcl-convert cannot create output directory structure at the path specified
by
giulia.trauzzi
▴ 10
Hi, thanks for this. I checked the permissions of the folder and changed them with chmod ugo+rwx /output_directory This has changed …
Comment: RNA-Seq analysis
by
carlopecoraro2
★ 2.5k
[Online course: ANALYSIS OF RNA SEQUENCING DATA WITH R/BIOCONDUCTOR][1] ---------- Dates 4-15 November 2024 [1]: https://www.physal…
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