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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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Answer: Constructing single sequence genome assembly out of short reads
by
Philipp Bayer
8.5k
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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Carlo Yague
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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…
Comment: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
dariober
14k
I guess the OP doesn't want to hard-code `p767.AM` and `"AM"`?
Comment: bcl-convert cannot create output directory structure at the path specified
by
marco.barr
▴ 140
I've never received this error before.. but you could try checking the permissions
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
gglim
▴ 140
``` library(dplyr) df %>% rowwise() %>% mutate(p767.AM = mean(c_across(contains("AM")))) ``` Maybe this is what you're looking for?
Answer: RNA-Seq analysis
by
Michael
54k
I think the situation you are finding yourself in is quite common. On a general note, as you are at the beginning of your PhD program, you …
Answer: RNA-Seq analysis
by
Nat.Nataren
▴ 30
We'll need a lot more information to help, you haven't given us much to work with. What organism are you working in? What is the experi…
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