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seen Sep 14 at 16:57

Programming, research in bioinformatics.


Sep
24
awarded  Autobiographer
Dec
9
awarded  Popular Question
Nov
18
awarded  Notable Question
Jul
9
awarded  Yearling
Mar
25
accepted How to find ion/water channel related genes
Mar
25
awarded  Popular Question
Jun
8
revised Too few transcripts from transcriptome assembler Oases
added 255 characters in body
Jun
8
comment Too few transcripts from transcriptome assembler Oases
Em, I tried to post to BioStar, but nobody answers me...
Jun
8
asked Too few transcripts from transcriptome assembler Oases
May
17
asked How to find ion/water channel related genes
Apr
26
revised Difference between strand-specific and not strand-specific RNA-seq data
added 11 characters in body
Apr
25
comment Difference between strand-specific and not strand-specific RNA-seq data
Thank you for your patience, @GWW. Yeah, the reads from antisense strand should be aligned to antisense DNA. So given a read, we KNOW that this read SHOULD be from which strand, right?
Apr
25
accepted Difference between strand-specific and not strand-specific RNA-seq data
Apr
25
comment Difference between strand-specific and not strand-specific RNA-seq data
I mean, you said "the reads derived from the antisense strand should align to the antisense strand of the genome", so what would Illumina provide? If they just provide whatever reads, that is not strand-specific, right? They must filter out sense or antisense reads, or they may mark each read as whether it is from sense or antisense strand. Am I right?
Apr
25
comment Difference between strand-specific and not strand-specific RNA-seq data
By the way, I checked the paper... But cannot find much regarding the post-processing of the data...
Apr
25
comment Difference between strand-specific and not strand-specific RNA-seq data
Thanks, @GWW. Does it mean that Illumina is going to provide two libraries (one antisense and one sense) to users? Or they just mark every read which sense it is from? When giving reads to customers, have they removed the adapters beforehand? Or users need to remove by themselves?
Apr
25
awarded  Editor
Apr
25
revised Difference between strand-specific and not strand-specific RNA-seq data
added 681 characters in body
Apr
25
comment Majority of transcripts are from sense strand?
Thanks, @Ben. I found this on Wiki: "The only real biological information that is important for labeling strands is the location of the 5' phosphate group and the 3' hydroxyl group because these ends determine the direction of transcription and translation." May I have this conclusion: the cell is going to read the DNAs ONLY from 5' end to 3' end, regardless whether it is reading the 5'->3' strand or 3'->5' strand? And whichever strand is used as a template to produce the transcript, it is called "antisense" strand? Moreover, when aligning, result "+" means aligned to sense strand?
Apr
25
comment Majority of transcripts are from sense strand?
Thanks, @biocs. Clearer now.