Hi, dsciATAC-seq team! I have encountered problems while using Bap2 bam to deal with the data in your manuscript. I ran the pipeline with SRR8310504_1.fastq.gz and SRR8310504_2.fastq.gz, according to the instructions in the Wiki page. The commnad I used was below:
mkdir -p 01.bap mkdir -p 01.bap/bapresults export PATH="/venv3/bin:$PATH" bap-barcode v2.1-multi -a ${sep=',' fastq1} -b ${sep=',' fastq2} --nmismatches 1 -o 01.bap/log -c ${cpp} zcat 01.bap/log-c*_1.fastq.gz > 01.bap/debarcode_1.fastq zcat 01.bap/log-c*_2.fastq.gz > 01.bap/debarcode_2.fastq bwa-mem2 mem -t ~{cpp} ~{refdir} 01.bap/debarcode_1.fastq 01.bap/debarcode_2.fastq | samtools view -bS - | samtools sort -@ 4 - -o 01.bap/sorted.bam samtools index 01.bap/sorted.bam bap-reanno -i 01.bap/sorted.bam -o 01.bap/CB_tag.bam -t CB samtools sort -@ 4 -o 01.bap/sorted_CB_tag.bam 01.bap/CB_tag.bam samtools index 01.bap/sorted_CB_tag.bam rm -rf 01.bap/log-c*_1.fastq.gz rm -rf 01.bap/log-c*_2.fastq.gz bap2 bam -i 01.bap/sorted_CB_tag.bam -o 01.bap/bapresults -c ~{cpp} -bt CB -w ~{whitelist} -bg /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/chrom_hg38-mm10.sizes -ts /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/tss.bed -bl /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/blacklist.bed --barcoded-tn5 -mc GRCh38
There were something differences like using bwa-mem2 but not bwa-mem, and mapping with my own genome.fa. Because I didn't know how to use bap2 bam to deal with mix cellline sample, I only use -mc GRCh38. And then I met the below error:
sorted_CB_tag.snakemake.log
So, what the errors mean in this log? How should I deal with this problem? @caleblareau
Hi, dsciATAC-seq team! I have encountered problems while using Bap2 bam to deal with the data in your manuscript. I ran the pipeline with SRR8310504_1.fastq.gz and SRR8310504_2.fastq.gz, according to the instructions in the Wiki page. The commnad I used was below:
mkdir -p 01.bap mkdir -p 01.bap/bapresults export PATH="/venv3/bin:$PATH" bap-barcode v2.1-multi -a ${sep=',' fastq1} -b ${sep=',' fastq2} --nmismatches 1 -o 01.bap/log -c ${cpp} zcat 01.bap/log-c*_1.fastq.gz > 01.bap/debarcode_1.fastq zcat 01.bap/log-c*_2.fastq.gz > 01.bap/debarcode_2.fastq bwa-mem2 mem -t ~{cpp} ~{refdir} 01.bap/debarcode_1.fastq 01.bap/debarcode_2.fastq | samtools view -bS - | samtools sort -@ 4 - -o 01.bap/sorted.bam samtools index 01.bap/sorted.bam bap-reanno -i 01.bap/sorted.bam -o 01.bap/CB_tag.bam -t CB samtools sort -@ 4 -o 01.bap/sorted_CB_tag.bam 01.bap/CB_tag.bam samtools index 01.bap/sorted_CB_tag.bam rm -rf 01.bap/log-c*_1.fastq.gz rm -rf 01.bap/log-c*_2.fastq.gz bap2 bam -i 01.bap/sorted_CB_tag.bam -o 01.bap/bapresults -c ~{cpp} -bt CB -w ~{whitelist} -bg /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/chrom_hg38-mm10.sizes -ts /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/tss.bed -bl /hwfssz1/ST_SUPERCELLS/P21Z10200N0090/huangzijie/shell/regions/blacklist.bed --barcoded-tn5 -mc GRCh38There were something differences like using bwa-mem2 but not bwa-mem, and mapping with my own genome.fa. Because I didn't know how to use bap2 bam to deal with mix cellline sample, I only use
-mc GRCh38. And then I met the below error:sorted_CB_tag.snakemake.log
So, what the errors mean in this log? How should I deal with this problem? @caleblareau