Dear all
I have in my project single end reads (100 bp) for some samples and paired end reads (100 bp frw and rev) for the other samples. I had to re-sequence some of the samples of which I have paired-end reads because the coverage was to low. However the re-sequence data I received back is single-end reads of 250 bp. Tophat wont allow mapping single and paired-end reads together. It says the result will look bad. They do mention that you can convert the junctions.bed file (output of Tophat) with bed_to_juncs using the -j option. I quote for TopHat manual "run TopHat on the 2nd set of reads using the -j option to supply the junctions file produced by be_to_juncs in the previous step". This is supposed to work but I didn't get it to work. Any suggestion on how I should go about analyzing this data?
Li
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM