sunta3iouxos

for some reason I am on the same boat. used --trim_poly_x and --trim_poly_g options  ./fastp -i A006850047_113702_S1_L002_R1_001.fastq.gz -o A006850047_113702_S1_L002_R1_001_trim.fastq.gz -I A006850047_113702_S1_L002_R2_001.fastq.gz -O A006850047_113702_S1_L002_R2_001_trim.fastq.gz --unpaired1 A006850047_113702_S1_L002_R1_001_unpaired.fastq.gz --unpaired2 A006850047_113702_S1_L002_R2_001_unpaied.fastq.gz --failed_out A006850047_113702_S1_L002_R2_001_failed.fastq.gz...

I am a bit confused. How do I update to the latest version? Am I using the: ``` library(remotes) install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler", "GuangchuangYu/enrichplot" )) ``` or something else?this might be relevant...

I would also like that

Thank you Phil for your time, Correct, I was refering to PhiX, typo! _[Edit: fixed in original post]_ > _"Those reads are typically removed in the demultiplexing step to generate...

Hi there, Have you found the answers to these? I am also wondering on the same. regards

> @Hoohm may I ask why the 9 trim. the inicial nucleotides are 10. @carbycrab could it be that the fastq file in addition to the CMOs has ADTs (CMOs...

> There are no specific settings. You can check #92 for some discussion on this topic. Hi @jsh58 #92 reefers to settings for CUT and **TAG**. The difference between the...

I have 64gb of memory. I am trying to index mm10 reference. What is the optimal amount of memory? Thank you for your time. On Mon, 31 Jul 2023, 9:58...

Good to know. Is there a possibility for these requirements to go even lower? Bwa 0.7.x can do the work easily with 8-16gb of memory On Wed, 2 Aug 2023,...

Hi Katarzyna, this is the error I get. Notice that the provided memory is: **mem_mb=115345, disk_mb=115345** ```bash ---- This analysis has been done using snakePipes version 2.8.1 ---- Sample sheet...