smithlabcode
about to-mr function
Hi. I am using gc_extrap to process some BAM files, and my version of Preseq is 3.2.0. According to your usage examples, BAM files need to be converted to MR files. However, I found that Preseq version 3.2.0 does not include a function to perform this conversion. While searching other websites, I discovered that Preseq previously had functions such as BAM2MR or to-mr, but these are not present in version 3.2.0. Currently, Preseq includes functions like c_curve, lc_extrap, gc_extrap, bound_pop, and pop_size. I am using Bedtools to convert these BAM files to BED files and then processing the BED files with the command 'preseq gc_extrap -B -o test1.txt test.bed' instead of using MR files. Can I run gc_extrap like this?
I have run the example data in your data directory using samtools and gc_extrap. This is my code : samtools sort -@ 30 -o SRR1106616_5M_subset.sort.bam SRR1106616_5M_subset.bam bedtools bamtobed -i SRR1106616_5M_subset.sort.bam > SRR1106616_5M_subset.sort.bed preseq gc_extrap -B -o testbed.txt SRR1106616_5M_subset.sort.bed. But I got a error: ERROR: reads unsorted in: SRR1106616_5M_subset.sort.bed prev = chr1 9807080 9807090 SRR1106616.105083640 255 + curr = chr1 9790490 9790500 SRR1106616.160558132 255 + Increase seg_len if in paired end mode
Is there a mistake in my process?