huangl07
huangl07
while？ how could I generate the bam file. I use the samtools sort and index it and I use the picard to MarkDuplicate should I use the sort bam file...
hear is my mapping script ` bwa mem ../Genome/ref.fa SRR5739123_1.fastq.gz SRR5739123_2.fastq.gz -t 4 -a -M -R "@RG\tID:SRR5739123\tLG:SRR5739123\tLB:SRR5739123\tPL:illumina\tSM:SRR5739123\tPU:run_barcode\tCN:MajorBio\tDS:reseq" | samtools view -bS > SRR5739123.bam samtools sort SRR5739121.bam -o SRR5739121.sort.bam samtools markdup...
well I think it's error maybe cause some low mapping quality reads or multimapping result `SRR5739119.25811182 401 NC_029256.1 1529566 0 125M NC_029259.1 5775201 0 * * NM:i:9 MD:Z:5G61C2A0C3A0A5G9G2A29 MC:Z:113M12AS:i:86 RG:Z:SRR5739119...
is there any one could solve it？
sorry bother that，but this reads also have error message
dear X-chen: I have already reanalysis other datas with the script like: 1st step: `bwa mem -M -a -t 8 -R "@RG\tID:1\tLG:A\tLB:1\tPL:illumina\tSM:A\tPU:run_barcode\tCN:MajorBio DS:reseq" /mnt/ilustre/centos7users/dna/SV/02.reference/ref.fa /mnt/ilustre/centos7users/dna/SV/data/B1228nova5:L1ECL171065:MJ20181118001:ECL171065:A.clean.1.fastq.gz /mnt/ilustre/centos7users/dna/SV/data/B1228nova5:L1ECL171065:MJ20181118001:ECL171065:A.clean.2.fastq.gz| samtools view -bS -...
e，the bam is generate by bwa mem -M -a -t 8 -R "@RG\tID:1\tLG:A\tLB:1\tPL:illumina\tSM:A\tPU:run_barcode\tCN:MajorBio DS:reseq" /mnt/ilustre/centos7users/dna/SV/02.reference/ref.fa /mnt/ilustre/centos7users/dna/SV/data/B1228nova5:L1ECL171065:MJ20181118001:ECL171065:A.clean.1.fastq.gz /mnt/ilustre/centos7users/dna/SV/data/B1228nova5:L1ECL171065:MJ20181118001:ECL171065:A.clean.2.fastq.gz| samtools view -bS - > /mnt/ilustre/centos7users/dna/SV/03.mapping/A.b1.bam samtools sort -o /mnt/ilustre/centos7users/dna/SV/04.sort/A.sort.bam --output-fmt BAM -@...
the bam is multiple record is it caused by the bwa -a parameter? I will check it!
Hi chen, good news is I remapping the read to generate the bam file without bwa men -a parameter but I can't understand why? could you show me some method...
could manta adapted bam files with all mapping data not only pared-end bams？