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ambj / MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
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Ensembl references and VEP #23

Open ambj opened 5 years ago

ambj commented 5 years ago

@ambj god, you are here, I am urgent for your help. no version of vep has the variant_effect_predictor.pl and variant_effect_predictor, what should i do, help, really very urgent. image image image

from the issue, I know you said you have tested ensemble_87, so I tried to keep the same with you, but I do not have fasta = /your/path/to/references/human_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fa chain = /your/path/to/references/human_GRCh37/liftover/hg19ToHg38.over.chain cDNA = /your/path/to/references/human_GRCh38/cDNA/Homo_sapiens.GRCh38.85.cdna.all.fa pep = /your/path/to/references/human_GRCh38/pep/Homo_sapiens.GRCh38.85.pep.all.fa cosmic = /your/path/to/references/cosmic/Census_allWed_Feb_17_09-33-40_2016.tsv

I tried to download the corresponding file, but I am afraid I am wrong. so I am here to confrim with you. http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz for chain what is worse, there are several files in ensemble_87, which file should I choose in fastq pep cdna. I list the link here, hope you can point out for me.

the worsest thing is that I know cosmic vcf file, but never use cosmic tsv file, so can you tell me where to download.

ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/pep/ ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/cdna/ ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/.

I send some emails to your eamil ambj@cbs.dtu.dk, I do not whether there is some bug in your school`s email, many days no reply.

I know my questions will waste you much time, sorry for disturb. wish you publish more CNS paper.

Originally posted by @2236529177 in https://github.com/ambj/MuPeXI/issues/14#issuecomment-453944577

ambj commented 5 years ago

Dear ?? I would prefer for you to keep the issue page clean - avoiding general question. Therefor i will delete this question from issue #14 .

I most politely ask for you to be patient and not send 4 emails and comment on the github page within one week. We are not employed as software supporters but researchers trying solve scientific questions and therefor do have other priorities.

Im very sorry if this have caused you inconvenience - we try to do your best.

For the questions:

please read the user manual carefully: https://github.com/ambj/MuPeXI/blob/master/doc/MuPeXI_User_Manual.md

here you will see that neither the cosmic, nor the chain liftover reference is necessary to run MuPeXI. you have provided the link to the rest of the dependent references yourself.

"I know my questions will waste you much time, sorry for disturb." - yes please be more patient and try to find answers and solve problems before contacting researchers.

I wish you the best of luck with your project.

Best, Anne-Mette