Closed gnilihzeux closed 3 months ago
my this data is not proper for circtools detect / DCC ? My other data works fine. But CIRI2 works fine either. My data throwing error were downloaded from ENA.
By the way, my STAR code:
if [[ -s $trim_fq1 && -s $trim_fq2 && ! -s ${align_bam}Chimeric.out.junction ]]
then
STAR --runThreadN 16 \
--genomeDir $STAR_INDEX \
--outSAMtype BAM SortedByCoordinate \
--readFilesIn $trim_fq1 $trim_fq2 \
--readFilesCommand zcat \
--outFileNamePrefix $align_bam \
--quantMode TranscriptomeSAM GeneCounts \
--chimOutType Junctions SeparateSAMold \
--outReadsUnmapped Fastx \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverLmax 0.05 \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--outSAMmultNmax 1 \
&> $log
fi
# Read1
if [[ -s $trim_fq1 && -s $trim_fq2 && ! -s ${align_bam_r1}Chimeric.out.junction ]]
then
STAR --runThreadN 16 \
--genomeDir $STAR_INDEX \
--outSAMtype None \
--readFilesIn $trim_fq1 \
--readFilesCommand zcat \
--outFileNamePrefix $align_bam_r1 \
--outReadsUnmapped None \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverLmax 0.05 \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--seedSearchStartLmax 30 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--outSAMmultNmax 1 \
&> $log_r1
fi
# Read2
if [[ -s $trim_fq1 && -s $trim_fq2 && ! -s ${align_bam_r2}Chimeric.out.junction ]]
then
STAR --runThreadN 16 \
--genomeDir $STAR_INDEX \
--outSAMtype None \
--readFilesIn $trim_fq2 \
--readFilesCommand zcat \
--outFileNamePrefix $align_bam_r2 \
--outReadsUnmapped None \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverLmax 0.05 \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--seedSearchStartLmax 30 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--outSAMmultNmax 1 \
&> $log_r2
fi
After review log, I found my _tmp_DCC/tmp_circCount
contains one line wired
chrM\t418\t15473\t-\tchrM\tchrM\tchrM\tchrM\tchrM\tchrM\tchrM\tchrM
Dear author,
I found a similar error with DCC 103. I'd tried all my efforts but could not solve it.
I had tried to install circtools from bioconda and pull down DCC from github. But all did't work.
Thanks
Describe the bug
My command
Desktop (please complete the following information):