Write more explicit installation and troubleshooting FAQs

[fabio-t]

[ginolhac]

Hi, thanks for developing such nice tool suite. Small comment, several tools like rgt-hint differential or rgt-hint footprinting which are using BAMs require that the BAM indexes are present. However, the error while indexes are absent are cryptic for the average user. Will be nice to check for indexes presences before any processing.

[lzj1769]

Hi, thanks for developing such nice tool suite. Small comment, several tools like rgt-hint differential or rgt-hint footprinting which are using BAMs require that the BAM indexes are present. However, the error while indexes are absent are cryptic for the average user. Will be nice to check for indexes presences before any processing.

Thanks for your suggestion. We now included the Index file checking in RGT. If the file doesn't exist, RGT will generate it with Pysam.

[umasstr]

Are there any instructions for the clone repo installation option? Pip installs often fail. It would be nice to be able to troubleshoot.

[ODream]

hello, for large bam file, the index is built by command like "samtools index -c xxx.bam". The index file is called "xxx.bam.csi". The codes in reg-gen/rgt/HINT/Footprinting.py (127-130), where only search "*.bai" index files, and built bam index without option "-c". Without changing the code, change the index file suffix from ".csi" to ".bai" could pass the index checking step.