Hi Brian. Yes, the reads have been adapter-trimmed. Moreover alignment toward long sequences (whole reference) gives good alignment rate and low while using short (miRBase) sequences.
-
-
Ahhh... to clarify, what I meant was NOT adapter trimming reads could cause the bias, but I guess that's out if the reads were successfully trimmed.Comment
-
I got this problem too. Did you figure out why exactly alignment is better for long sequences than miRBase?Comment
-
Please don't align directly to the mature.fa, only about 50% of miR reads are the exact mature sequence, you are missing a lot of sequence diversity that will map clearly to the harpin.fa. Calling 3p and 5p arm switching on the other hand, that's a different story.Originally posted by moses122 View PostComment
-
Thanks for replying. I did mapped to hairpin.fa. The alignment rate is only around 0.01% and it's 90% for genome. I used bowtie and allowed one mismatch.Originally posted by mziemann View PostComment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment