how to "merge" ?

[zdWang04]

Hello,

I recently encountered a problem while using your software. I would like to analyze paired-end sequencing data, but I noticed that the parameter section only supports single-end sequencing. For paired-end sequencing, it seems that I need to run the program separately and then merge the results. What would be the best way to perform this "merging"? For example, should I use intersection, union, or another method?

Thank you!

[rna-editing1]

You are right; analyzing stranded, paired-end data is not supported out of the box.
As a workaround you can analyze the *_1.fastq and *_2.fastq individually:

• Align these fastq files separately to obtain one bam file per fastq file.
• Identify each file's strandedness/library type (manually in a genome browser or automatically via tools like salmon or how_we_are_stranded_here).
• Organize and group your bam files by identified library type.
• Run LoDEI for all files with identical library type.
• Filter results according to your q-value threshold.
• Merge the results, e.g., by using bamtools intersect.

There is no right or wrong when deciding between an intersection or a union. However, an intersection seems helpful in only keeping window regions covered in both result files.

[zdWang04]

You are right; analyzing stranded, paired-end data is not supported out of the box. As a workaround you can analyze the *_1.fastq and *_2.fastq individually:

• Align these fastq files separately to obtain one bam file per fastq file.
• Identify each file's strandedness/library type (manually in a genome browser or automatically via tools like salmon or how_we_are_stranded_here).
• Organize and group your bam files by identified library type.
• Run LoDEI for all files with identical library type.
• Filter results according to your q-value threshold.
• Merge the results, e.g., by using bamtools intersect.

There is no right or wrong when deciding between an intersection or a union. However, an intersection seems helpful in only keeping window regions covered in both result files.

thanks for your replying!