Cai Shaojiang

109 reputation

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	109 reputation	bio	website		visits	member for	1 year
5 badges		location			seen	Apr 19 at 5:15

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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.
Apr 25	accepted	Majority of transcripts are from sense strand?
Apr 25	awarded	Scholar
Apr 25	accepted	Purpose of poly(A)+ RNA?
Apr 25	comment	Majority of transcripts are from sense strand? Thanks, GWW. Maybe I was wrong, i thought the "anti-sense strand" as the 3'->5' strand. So you mean, for example, the DNA is "AAAAATTTTT", some transcript could be "AATTT" and some could be "TTTAA"? Could you please further clarify it?