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2 hours ago by


I am getting the following error when I try to use the Stringtie merge function stringtie --merge -p $threads -G DM_1-3_516_R44_potato.v6.1.working_models.gff3 -o stringtie_merged.gtf mergelist.txt.

Error: the input alignment file is not sorted!
Alignments (7) already found for scaffold_128 !

As mentioned in previous posts I checked the indexed bam files and they look fine. Please see below.

  $ samtools view -H PVX_2d_1.bam | grep "HD"


@HD VN:1.0 SO:coordinate

I checked the mergelist.txt and there are no empty spaces nor empty lines. There I have twelve samples.
Before merge step I assembled transcripts using stringtie --rf -p $threads -G DM_1-3_516_R44_potato.v6.1.working_models.gff3 -o ${SAMPLE}.gtf -l ${SAMPLE} ${SAMPLE}.bam using indexed bam files.

Can someone help me in this regard?
Thanks in advance.

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