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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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error when using convert-sam-for-rsem to a RSEM compatible BAM file. #208

Open qxf1995 opened 7 months ago

qxf1995 commented 7 months ago

Hi, I want to convert my bam file to satisfy RSEM's requirement. Then I want to use rsem-calculate-expression command to estimate gene and isoform expression from RNA-Seq data. What can I do with this problem?

samtools sort -n -@ 1 -m 1G -o PA_5.AddRG.Reorder.convert_forRSEM.tmp.bam /storage2/workspace/RNAseq_SED_vs_PA/data/F23A430002092_MUSfxwlT/Alignment_hisat/bam/PA_5.AddRG.Reorder.Sort.bam [bam_sort_core] merging from 13 files and 1 in-memory blocks...

rsem-scan-for-paired-end-reads 1 PA_5.AddRG.Reorder.convert_forRSEM.tmp.bam PA_5.AddRG.Reorder.convert_forRSEM.bam ....................... Finished!

Conversion is completed. PA_5.AddRG.Reorder.convert_forRSEM.bam will be checked by 'rsem-sam-validator'. rsem-sam-validator PA_5.AddRG.Reorder.convert_forRSEM.bam . The two mates of paired-end read V350220273L3C001R00100223784 are not adjacent! The input file is not valid!