Question: The problem with RSEM
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gravatar for 498476732
2.7 years ago by
4984767320
4984767320 wrote:

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 !

rna-seq • 1.4k views
ADD COMMENTlink written 2.7 years ago by 4984767320

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.

ADD REPLYlink written 2.7 years ago by i.sudbery4.3k
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