So I want to analyze the gene expression from a specific cluster of genes interest, and I took the samples from a different tissue, all of them from SRA data tables, however, my samples are some of them 4 replicates, and other tissue samples only 2 and 3 replicates, do you think I still can proceed my analysis? is really difficult for me to find 4 replicates...

Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance works just fine, but I can't figure out how to clip the opposite end as well (with reads having different lengths). Thanks!

This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without assigning them to mother or fetus. The result would be unique reads from one person, unique reads for the other, and shared reads.

> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) data available for the mother?

I can also suggest which links TFs to their DNA motifs, not their gene targets.