How to solve the problem of establishing refFlat.txt file

This article mainly explains how to solve the problems in the establishment of refFlat.txt files. The content of the explanation is simple and clear, and it is easy to learn and understand. Please follow the editor's way of thinking to study and learn how to solve the problems in the establishment of refFlat.txt files.

Transcriptome index

Command for statistical gene coverage ratio: / share/work/biosoft/java/jre1.8.0_73/bin/java-jar / share/work/biosoft/picard/picard-tools-2.1.0/picard.jar CollectRnaSeqMetrics REF_FLAT=/share/work/database/ref/Saccharomyces_cerevisiae/Yeastgenome/refFlat.txt INPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/1.Mapping/3ts-30min/3ts-30min .bam OUTPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/2.Map_stat/3ts-30min.map_base.stat CHART_OUTPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/2.Map_stat/3ts-30min.Normalized_Distance_Along_Transcript.pdf STRAND_SPECIFICITY=NONE VALIDATION_STRINGENCY=LENIENT

An error occurs due to too few lines in the refFlat.txt file:

Check the reason:

An error was reported when the file was generated, resulting in too few gene regions

GtfToGenePred-genePredExt saccharomyces_cerevisiae.gtf refFlat.tmp.txtno exons defined for group HRA1, feature noncoding_exon (perhaps try-ignoreGroupsWithoutExons)

Improvements:

GtfToGenePred-genePredExt-ignoreGroupsWithoutExons saccharomyces_cerevisiae.gtf refFlat.tmp.txt thank you for reading, the above is the content of "how to solve the problems in the establishment of refFlat.txt documents". After the study of this article, I believe you have a deeper understanding of how to solve the problems in the establishment of refFlat.txt documents, and the specific use needs to be verified in practice. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!