Hello, I would like to ask your help to understand why you preferred adding "split" parameter to get the intersection between the bam files and ucscHg38Alu.bed.gz file in the first step. Based on the bedtools documentation when this parameter is used, only the intersects within the exonic region would be considered; however, there are cases RNA-editing sites within intronic regions that also overlap with Alu repeats. May I learn what is your concern about eliminating those intronic RNA-editing sites? Also, unfortunately, if I used samtools version higher than 1.8 with bedtools/2.26, I get the error samtools sort: failed to read header from "-" after running line 7th within FullConfigStranded.ini script. If I use samtools 1.8 with bedtools/2.26, it does not give me an error but I do not get any output. When I remove the split parameter, it works without any problem. Many thanks in advance for your help!
Hello, I would like to ask your help to understand why you preferred adding "split" parameter to get the intersection between the bam files and ucscHg38Alu.bed.gz file in the first step. Based on the bedtools documentation when this parameter is used, only the intersects within the exonic region would be considered; however, there are cases RNA-editing sites within intronic regions that also overlap with Alu repeats. May I learn what is your concern about eliminating those intronic RNA-editing sites? Also, unfortunately, if I used samtools version higher than 1.8 with bedtools/2.26, I get the error
samtools sort: failed to read header from "-"after running line 7th within FullConfigStranded.ini script. If I use samtools 1.8 with bedtools/2.26, it does not give me an error but I do not get any output. When I remove the split parameter, it works without any problem. Many thanks in advance for your help!