Hi all,
I have a few questions about the metadata file.
1) Why are the counts in the TotalReads and MappedReads columns the same? Do the fastq files only contain aligned reads and if so, is there anywhere I can download the raw fastq files?
2) Should the counts in the Number of dup readSamtools and Unique ReadsSamtools columns add up to the TotalReads column?
3) I downloaded UMB5558_ba9.R1.fastq (syn7115553) and UMB5558_ba9.R2.fastq (syn7115558) and and saw that there are 40827567 total reads. However, this number doesn't appear at all in the corresponding row in the metadata file (it says there are 62497085 total reads). Does anyone know what might be the cause of this discrepancy?
4) Why are the counts in TotalReads less than the counts in the Reads after rmdup-Samtools column?
Thank you!
Best,
Elaine