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Hi <@U03CKGEU3LZ>, regarding the test data, turns ...
# drop
a
Hi @Nicolas Vannieuwkerke, regarding the test data, turns out that one of our colleges has already aligned 120 of the samples from 1000-genomes-project and we have the bam files ready on our clusters. What is the status on your side? if you haven't started maybe we can simply use them?
n
Oh that would be perfect! I haven't had time to start with it yet 🙂
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a
Then probably I would just need some links/instruction on how I can deposit the data easily from our cluster to aws
n
I'll ask around, hang on 😛
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Okay so we determined that it would be best that I upload the data. Do you have an easy way to send the data to me? In the meantime I'll do a run of the pipeline to create the count files so we can limit the amount of BAM file uploads
a
I can't think of an easy way😅 I can probably put 10 of them at a time to my google drive and share it with you that way?
n
allright 😛 how big are the files?
a
around ~4G per each bam
n
Oof that's a lot of data 😁
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a
I think we should aim for only 50 samples if possible to get meaningful results.
n
yeah that might be best, those tests don't need to actually produce usable results. It just needs to test and show what the pipeline does on full data
d
Thanks for taking care of this both! I just had a comment to Nicolas' last comment. You're right we don't need "usable results" for the test but we do want to ensure there is enough data to produce some outliers (expression and splicing) so that there aren'tn empty tables and some modules don't get tested. Right?
n
Yes preferably indeed 😛
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a
n
Thanks I'll try and download it now
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All files have been downloaded 😛 Ready for the next batch
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a
Do we need more bam files? I also think we can simply count the others and use them as external files.
n
Yes that might be easier! You can also send those to me. Could you also send the used references so there is no mismatch there?
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a
Amazing. We are having a hackathon this week at our lab. I will send them to you probably on Monday.
n
Perfect, no rush. Have fun at your hackathon!
a
They have been counted by gencode V44. We have to set this exact version also for the bam files
The bam files were mapped to 
GRCh38.p14.genome.fa.gz
, also using 
gencode.v44
and 
star_salmon
aligner using nf-core/rnaseq pipeline.
n
Thanks I'll take a look at it tomorrow
a
Thanks!
n
Sorry I'm a bit held up, I'll try and do the download and transfer tomorrow
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Okay I uploaded all the data! Could you also send me the exact reference data used to generate the BAM files and counts? (Links are also fine here). That should be the last files necessary to set up the full test
a
The gtf is from gencode: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.chr_patch_hapl_scaff.annotation.gtf.gz and I think the reference is here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/ The name of the file in the nextflow config is 
GRCh38.p14.genome.fa.gz
I'm pretty sure this should be it but I can also make sure on Monday
n
Thanks! I'll give it a go today
https://github.com/nf-core/drop/pull/96 There's something broken in the megatests atm, I'll keep you up to date
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