Open El-Castor opened 1 year ago
Hi,
As recommanded by mehlan, I open an issue related to filterbam script use.
I have aligned the RNA-seq paired reads using tophat following this command:
# Running TopHat: tophat -o $outputDIR1/ -p 16 $index_DIR/dgl_COI_bwt_index $RNAseq_leaves_interleave # convert junction bed file from the first run: junction_bedFile_PATH=$outputDIR1/junctions.bed cat $junction_bedFile_PATH | python2 /NetScratch/cpichot/.conda/envs/tophat/bin/bed_to_juncs > $outputDIR1/junctions_parsed.bed RNAseq_roots_interleave=$RNAseq_files_DIR/SRR1664818_Pisum_sativum_cv_Cameor_Root_system_paired_end_library_stage_A_High-nitrate_Hydroponics_readNameChanged_interleave.fastq.gz tophat -j $outputDIR1/junctions_parsed.bed -o $outputDIR2/ -p 16 $index_DIR/dgl_COI_bwt_index $RNAseq_roots_interleave
After Alignment I sort the bam file from topHat using samtools following this command:
conda activate samtools align_results_bam_leaves_PATH=$outputDIR1/accepted_hits.bam align_results_bam_root_PATH=$outputDIR2/accepted_hits.bam samtools sort -n $align_results_bam_leaves_PATH > $outputDIR1/accepted_hits.s samtools sort -n $align_results_bam_root_PATH > $outputDIR2/accepted_hits.s conda deactivate
And then I try to filtered the bam files using filterBam script following this command:
conda activate Augustus #samtools sort -n -o $outputDIR1/accepted_hits.s.bam $outputDIR1/accepted_hits.bam # recommandation of mehlan filterBam --verbose --uniq --paired --in $outputDIR1/accepted_hits.s.bam --out $outputDIR1/accepted_hits.sf.bam --pairwiseAlignments filterBam --uniq --paired --in $outputDIR2/accepted_hits.s --out $outputDIR2/accepted_hits.sf.bam --pairwiseAlignments conda deactivate
Unfortunatly I have segmentation fault error as you can see bellow :
filterBam --verbose --uniq --paired --in $outputDIR1/accepted_hits.s.bam --out $outputDIR1/accepted_hits.sf.bam ------------------------------------------------ Selected options are: best=0 help=0 noIntrons=0 paired=1 uniq=1 verbose=1 pairwiseAlignments=0 Input file: /NetScratch/FLOCAD/cpichot/genome_assembling/2-geneAnnotation/topHat_out_leaves/accepted_hits.s.bam Output file: /NetScratch/FLOCAD/cpichot/genome_assembling/2-geneAnnotation/topHat_out_leaves/accepted_hits.sf.bam insertLimit=10 maxIntronLen=500000 minCover=80 minId=92 minIntronLen=35 uniqThresh=0.96 commonGeneFile= pairBedFile= ------------------------------------------------ Erreur de segmentation
I dragged the bam file so you can check it bamfiles.zip
Do you have any recommendation, or see what I am doing wrong ?
Thanks in advance
up ?
Hi,
As recommanded by mehlan, I open an issue related to filterbam script use.
I have aligned the RNA-seq paired reads using tophat following this command:
After Alignment I sort the bam file from topHat using samtools following this command:
And then I try to filtered the bam files using filterBam script following this command:
Unfortunatly I have segmentation fault error as you can see bellow :
I dragged the bam file so you can check it bamfiles.zip
Do you have any recommendation, or see what I am doing wrong ?
Thanks in advance