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Dear Christoph and Swati,
I used the new version zUMIs today with the example data but got a strange error which didn't occur in the last zUMIs version. On our server, the previous version of zUMIs…
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I am trying to run the [amazon_ec2](https://github.com/radical-cybertools/saga-python/blob/devel/examples/resource/amazon_ec2.py) script (again!), but I get an error indicating that SAGA cannot detect…
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Hi, I have scRNAseq data with cell barcode and UMI in the Barcode read and and an additional plate barcode at the end of the cDNA read. I can extract the plate barcode from the cDNA read in a preproce…
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Hi! Thanks for this great tool.
Do you have any suggestions on the inputs to zUMI for split-seq data? The barcodes we have for each cell is 18 bp long, but is separated every 6 basepairs by a gap …
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Dear zUMIs developers,
I managed to run zUMIs with example data you provided on the EC2 instance, and everything was good! Later, I've tried it with one lane of the 10x t_4k dataset (approx. 4GB):
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When running:
$ MPIR_CVAR_OFI_USE_PROVIDER=verbs srun -n 90 -N 45 osu_alltoall
I hit an abort() on a few nodes:
(gdb) bt
#0 0x00007ffff3ea65f7 in raise () from /lib64/libc.so.6
…
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Dear zUMIs developers,
I've been trying to run zUMIs with this command line:
`bash ./zUMIs/zUMIs-master.sh -f ./zUMIs/ExampleData/barcoderead_HEK.1mio.fq.gz -r ./zUMIs/ExampleData/cDNAread_HEK.1…
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Dear zUMIs developers,
I am trying to apply zUMIs to a non standard scRNAseq protocol (https://www.nature.com/articles/s41467-017-00244-w.pdf). I think zUMIs should not have a problem with such da…
ghost updated
6 years ago
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I am using the following syntex to run zUMIs:
bash $p/zUMIs-master.sh -f /private/zel/tom/mike3/LIB030951_GEN00110820_S1_L001_R1.fastq \
-r /private/zel/tom/mike3/LIB030951_GEN00110820_S1_L001_R2.…
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Hello!
When I ran the zUMIs in a server with the use of example data. I got an error message:
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ln: failed to create symbolic link 'path/to/chr22test.aligned.sorted.bam.i…