gunzip -c chr*.fa.masked > hg19.fa

[zhenzuo2]

Hello,

When I run

gunzip -c chr*.fa.masked > hg19.fa

in CENTIPEDE.tutorial in Genomic sequence Section, I got the following error

gzip: chr10.fa.masked: not in gzip format
gzip: chr11.fa.masked: not in gzip format
gzip: chr11_gl000202_random.fa.masked: not in gzip format
...

Am I doing it wrong? Thanks.

[slowkow]

Yes, gzip will throw that error when you try to decompress (gunzip) a file that is not compressed.

You only need to decompress a file when it is compressed (it will have the .gz file extension).

[slowkow]

I think you caught a typo in my tutorial! Thanks for reporting it.

I haven't tested it, but I think the correct command is:

cat chr*.fa.masked > hg19.fa

Good luck! Let me know how it goes. Thanks again for reporting the problem.

[zhenzuo2]

Thank you so much for your prompt reply. Your tutorial is the best tutorial I can find online. It helps a lot for beginners like me.

I also have a question about where to download ENCFF001UUQ.narrowPeak.gz and ENCFF001UUQ_gt8.narrowPeak.gz. You explained it in DNase-Seq data section but I am still not very sure where to find them. Thanks.

[slowkow]

It looks like the particular files I used in the tutorial have been archived.

You should find a different study that interests you:

https://www.encodeproject.org/search/?type=Experiment&assay_term_name=DNase-seq&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens

Here is one possible example, showing the links to the BAM file and the narrowPeak bed file:

[zhenzuo2]

Thank you a lot. It makes sense now.

Best,

Zhen