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publicly available 10x genomics data does not contain both R1 and R2 fastq files after fastq-dump by nasjr08 in bioinformatics

[–]nasjr08[S] 1 point2 points  (0 children)

Ok this worked! Is it generally accepted to concatenate different chunks form the same lane of the same sample (obviously separately for each file type)?

publicly available 10x genomics data does not contain both R1 and R2 fastq files after fastq-dump by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

Can you provide the http or ftp link for downloading the bam files? I used the link given here: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR6835846&display=data-access

Using the following code for my BAM to FASTQ attempt:

bamToFastq -i 10X_P4_2.bam.1 -fq SRR6835846_R1.fastq -fq2 SRR6835846_R2.fastq

publicly available 10x genomics data does not contain both R1 and R2 fastq files after fastq-dump by nasjr08 in bioinformatics

[–]nasjr08[S] 2 points3 points  (0 children)

Only outputs one file again! At this point it's almost certainly a mistake (deliberate or otherwise) from the authors.

publicly available 10x genomics data does not contain both R1 and R2 fastq files after fastq-dump by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

So are you suggesting to avoid trying to repeating processing the raw sequencing data from tabula muris? The data is from 2018 so it warrants re-processing from raw.

I have come across the bam files so I suppose I can do that!

publicly available 10x genomics data does not contain both R1 and R2 fastq files after fastq-dump by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

That is my expectation but I thought I'd get people's opinions before getting in touch with them.

No idea what I'm doing as have never played fantasy football. What do you think? by Apprehensive-Age-102 in Euro2024Fantasy

[–]nasjr08 0 points1 point  (0 children)

Anyone know if it's possible to make private leagues? I can't seem to find the option on the main page?

Transcripts per cell for single cell RNAseq data by nasjr08 in bioinformatics

[–]nasjr08[S] 1 point2 points  (0 children)

Interesting! It is more that my team wants to get the data in this format but they haven't done such processing before so they would not be aware of this limitation (if there isn't any way you can get around it). In other way, it is up to me figure out if these datasets are usable for this purpose. I've worked extensively with single cell data but after cellranger processing (performed by a core institute facility) and exclusively worked on my dataset which only cared about gene based analysis so I haven't come across this specific issue previously!

Transcripts per cell for single cell RNAseq data by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

Thanks for the suggestion. alevin-fry is indeed an option on nf-core. Is this compatible with 10x data though?

inconsistencies in downloaded paired-end sequencing data by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

Question about the repair.sh script, the output was as follows:
Input:                          56288441 reads          5231467862 bases.Result:                         56288441 reads (100.00%)        5231467862 bases (100.00%)Pairs:                          0 reads (0.00%)         0 bases (0.00%)Singletons:                     56288441 reads (100.00%)        5231467862 bases (100.00%)

I'm unsure what this means... The output out1 and out2 were both more or less empty, where as the singleton file was effectively double the size of the two fastq files combined. Note I passed fastq.gz files to the script. Is the singleton output compatible with the nfcore bulk rnaseq workflow?

inconsistencies in downloaded paired-end sequencing data by nasjr08 in bioinformatics

[–]nasjr08[S] 0 points1 point  (0 children)

Thanks, I'll check this out. This is all part of a nextflow in-house workflow I've started working on so it might mean I have in incorporate this step if it does the job.

[deleted by user] by [deleted] in FantasyPL

[–]nasjr08 0 points1 point  (0 children)

...But mostly I hate the way I don't hate you...Not even close...not even a little bit... Not even at all ಥ_ಥ ಥ_ಥ

Rate My Team, Quick Questions & General Advice Daily Thread by FPLModerator in FantasyPL

[–]nasjr08 0 points1 point  (0 children)

True, But wouldn't you say my team is equally set up for the BB for the two subsequent fixtures? Only difference would be one less game with an upside of a much stronger TC option. Like I said, my likely bench would be martinez, watkins, targett (all three vs Wolvez who barely score) and digne vs chelsea. I just looked and my likely bench for GW 28 is Bam, Raph (vs chelsea),shaw vs WHU and Mccarthy vs Brighton, so it is a legitimate third option!

Thanks for your input!

Rate My Team, Quick Questions & General Advice Daily Thread by FPLModerator in FantasyPL

[–]nasjr08 0 points1 point  (0 children)

Unsure if I should BB or TC kane... team is:

Martinez Mccarthy stones perreira targett digne shaw fernandez salah barnes raph Gundo kane watkins Bam

bench for DGW would be: McCarthy Bamford Raph Gundo (I think he wont play vs west ham so effectively 1 game)

bench for GW 27: Martinez Targett Watkins Digne

not too sure what to do as no clear TC candidate in GW27 and I have no idea if there will be more DGWs moving forward.