GRCh38_nestedRepeats_20200703.tsv in update version or nested_repeat_file=/path/to/nested/repeat.tsv in initial version

MarioniLab / CELLOseq

Transposable element expression at unique loci in single cells with CELLO-seq

MIT License

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GRCh38_nestedRepeats_20200703.tsv in update version or nested_repeat_file=/path/to/nested/repeat.tsv in initial version #1

Open Kratos12138 opened 1 year ago

Kratos12138 commented 1 year ago

Hi andr-kun,

I am trying to replicate your script manuscript/bash_files/TE_isoform_filter/transposon_isoforms_filter_hipsci.sh but I am having trouble finding the file GRCh38_nestedRepeats_20200703.tsv. I have searched for it on Google and UCSC, but I couldn't find a suitable download link. Can you please share the download link for this file? I would really appreciate it.

Thank you.

andr-kun commented 1 year ago

Hi Kratos12138,

You can download the nested repeats file from UCSC genome browser, using their table export tool. The specific options you need to download the nested repeats file for the hipsci analysis can be found in the image below:

Screenshot 2023-04-04 at 10 29 36

Kind regards, Andrian