Open bioinfo89 opened 3 years ago
Hi,
I get the below mentioned error when I try to run Chiapet2 tool on subsampled reads. It was running fine for the reads before. Following is the command I am using:
seqtk sample -s100 SRR_1.fastq.gz 0.1 >R1_1_sub0.1.fastq seqtk sample -s100 SRR_2.fastq.gz 0.1 >R2_2_sub0.1.fastq
ChIA-PET2-0.9.3/bin/ChIA-PET2 -t 10 -g hg19.fa -b hg19.chrom.sizes -f R1_1_sub0.1.fastq.gz -r R2_2_sub0.1.fastq.gz -m 1 -A CGCGATATCTTATCTGACT -B GTCAGATAAGATATCGCGT -e 2 -k 2 -l 12 -C 1 -o 0.1 -n ChIAPETV2_0.1
Error message: ERROR: The input file is neither a BAM file nor a SAM file.
Hi,
I get the below mentioned error when I try to run Chiapet2 tool on subsampled reads. It was running fine for the reads before. Following is the command I am using:
seqtk sample -s100 SRR_1.fastq.gz 0.1 >R1_1_sub0.1.fastq seqtk sample -s100 SRR_2.fastq.gz 0.1 >R2_2_sub0.1.fastq
Running ChIA-PET2 :
ChIA-PET2-0.9.3/bin/ChIA-PET2 -t 10 -g hg19.fa -b hg19.chrom.sizes -f R1_1_sub0.1.fastq.gz -r R2_2_sub0.1.fastq.gz -m 1 -A CGCGATATCTTATCTGACT -B GTCAGATAAGATATCGCGT -e 2 -k 2 -l 12 -C 1 -o 0.1 -n ChIAPETV2_0.1
Error message: ERROR: The input file is neither a BAM file nor a SAM file.