The problem with RSEM
Hello! Thanks for taking the time to read ,I use RSEM to calculate gene expression ,but there were some errors , I tried to prepare reference sequence by using rsem-prepare-reference program. My operation as follows: $ rsem-prepare-reference --bowtie2 --bowtie2-path bowtie/bowtie2-2.1.0/bowtie2 refGene/refGene.fa ref/10M_reference $ rsem-calculate-expression -p 8 --paired-end --bam SRA/SRR192333_bwt.bam ref/10M_reference SRA/SRR192333_rsempaired_end_quals
Then the error which pasted here was shown in terminal: RSEM does not support gapped alignments, sorry! I don't konw how to solve it , so I ask you for help !
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How did you obtain your BAM file? It looks like it was produced with parameters incompatible with RSEM. SPecifically, it looks like it has been mapped with a gapped aligner when RSEM does not support gapped alignments.