how to get ecc reads from Circle-map outputs file about circle-map

[iprada]

Dear @panxiaoguang

You are right. Circle-Map Realign provides a summarized output of the eccDNA reads.BUt it does not provide direct access to the reads.

I have a beta release of that reports the output realigned in reads in BAM format, following the standard SAM format to report the realigned reads as split reads. I think that this is exactly what you are looking for. You can execute it as follows:

Circle-Map bam2bam -i sorted_circular_dna_candidates.bam -qbam qname.bam -fasta /path/to/hg38.fa -o output.bam 

Where:

sorted_circular_dna_candidates.bam: Is the same input as Circle-Map Realign
qname.bam is a query name sorted bam file

Best,

Inigo

[panxiaoguang]

Thank you very much for your reply

[panxiaoguang]

Hi, Inigo,

after running Circle-Map bam2bam, I successfuly got a bam file. But when I run samtools sort, I got an error message "[E::bgzf_read_black] Invalid BGZF header at offset 1203765486". Have you ever encountered this error, and what are the possible reasons?