Hi all, I have some questions regarding this dataset. After running fastqc, my team realized that there were some disparities in read length. Some samples have different read lengths in metadata as compared to fastqc results. I also would like to know if the samples are reverse or forward and are all of them rRNA-depleted. Thank you in advance!
Created by Jenny Empawi jaempawi Thanks so much for the IDs. I've looked into this a little bit, so in answer to your questions:
1. In the metadata file (syn26254718), the `readStrandOrigin` column should tell you whether each sample was forward or reverse.
2. I don't see any info on whether they are rRNA depleted on Synapse or in their paper, so I can't answer this question. You will have to contact the data contributor (info below).
3. I'm not sure why the read lengths differ between the metadata and fastq files, but it's possible that the metadata file could be wrong. I would ask the data contributor about this as well.
The person to ask about this is Roman Kosoy from MSSM: roman.kosoy@mssm.edu
I hope that helps!
Jaclyn Hello Jaclyn.
Thanks for replying! These are two of the some fastq files that appear to have different read lengths: syn26250847, syn26250849 and this is the metadata corresponding to it.
Best,
Jenny Hello,
Can you please tell me the Synapse IDs of some of the fastq files and metadata? Otherwise I can't find the data set you are looking at.
Thank you!
Jaclyn