use uBAM in docs and provide link to explanation

Author: sreichl

README.md

@@ -65,7 +65,7 @@ The processing and quantification described here was performed using a publicly
 
 # 🚀 Features
 - Processing (`results/`)
-    - Alignment of both single-end and paired-end reads in raw/unaligned BAM format with Bowtie2.
+    - Alignment of both single-end and paired-end reads in raw/unaligned/unmapped [uBAM](https://gatk.broadinstitute.org/hc/en-us/articles/360035532132-uBAM-Unmapped-BAM-Format) format with Bowtie2.
       - Filtering using `samtools view` can be configured using [SAM Flags](https://broadinstitute.github.io/picard/explain-flags.html) (`SAM_flag`).
     - Peak calling with `MACS2`.
       - Duplicate handling can be configured using `macs2_keep_dup`.

config/README.md

@@ -6,7 +6,7 @@ You need one configuration file and one annotation file to run the complete work
 - annotation.csv: CSV file consisting of one technical sequencing unit per row (i.e., one sample can include multiple sequencing units, hence mutliple rows) and 4 mandatory columns:
   - sample_name (first column!)
   - read_type: "single" or "paired".
-  - bam_file: path to the raw/unaligned BAM file.
+  - bam_file: path to the raw/unaligned/unmapped [uBAM](https://gatk.broadinstitute.org/hc/en-us/articles/360035532132-uBAM-Unmapped-BAM-Format) file.
   - pass_qc: number between 0 (not used for downstream steps e.g., quantification) and 1. Every sample with pass_qc>0 is included in the downstream quantification and annotation steps.
   - (optional) additional sample metadata columns can be added and indicated for inclusion in the report.