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xflicsu gevaertlab zm-git-dev wangdi2016 genomicsnx

rnaseq_pipeline's Issues

How create the "Homo_sapiens_assembly38.fasta" file in the "prepare_reference/run_reference.sh"

Dear zheng:

When we prepared the RNASeq_pipeline, we encounted an error with running this CMD $gffread NONCODEv5_human_hg38_lncRNA.gtf -g Homo_sapiens_assembly38.fasta -w NONCODEv5_human_hg38_lncRNA.fa from "prepare_reference/run_reference.sh line 41". We have replaced the Homo_sapiens_assembly38.fasta to GRCh38.primary_assembly.genome.fa, but it didn't work and output an error Warning: couldn't find fasta record for 'chr4_GL000008v2_random'! Error: no genomic sequence available (check -g option!). . Would you like to help us to work out how to create this file Homo_sapiens_assembly38.fasta?

Thank you so much!

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