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Forum: RNA Sequencing 08-29-2015, 07:47 PM
Replies: 2
Views: 2,270
Posted By skly
Thanks dpryan~ I am clear.

Thanks dpryan~
I am clear.
Forum: RNA Sequencing 08-29-2015, 06:56 PM
Replies: 2
Views: 2,748
Posted By skly
Yes, I checked the input files and found that I...

Yes, I checked the input files and found that I had a mistake~ :eek:
Thank U, dpryan.:)
Forum: RNA Sequencing 08-28-2015, 12:38 AM
Replies: 2
Views: 2,270
Posted By skly
masked or unmasked genome reference for RNAseq

Hi guys.
I aligned RNAseq data to unmasked genome and hard masked genome, respectively. The mapping rate of the the former was about 92% and the latter rate was about 75%. It seemed that about 20%...
Forum: Introductions 08-27-2015, 10:35 PM
Replies: 4
Rna
Views: 1,213
Posted By skly
Thank you, dpryan. I replaced the masked...

Thank you, dpryan. I replaced the masked reference with unmasked genome reference. The mapping rate was about 90%, but I found one another question. The discordant alignment rate was so high. The...
Forum: RNA Sequencing 08-27-2015, 10:15 PM
Replies: 2
Views: 2,748
Posted By skly
HISAT Discordant Alignment Rate of RNAseq data was so high

To run fast and test the result, I splited one paired-end RNAseq fastq to eight pairs, then I aligned the data to unmasked genome reference using HISAT and Tophat2 respectively. It was so strange...
Forum: Introductions 08-26-2015, 05:59 AM
Replies: 4
Rna
Views: 1,213
Posted By skly
Thank you, dpryan! Actually, these RNA...

Thank you, dpryan!
Actually, these RNA sequencing data have be removed the adapter and be filtered low quality reads.
I suspected that HISAT caused the low mapping rate, firstly. So, for...
Forum: Introductions 08-23-2015, 06:35 PM
Replies: 4
Rna
Views: 1,213
Posted By skly
Rna

I aligned RNA sequenceing data to human genome using HISAT. To my surprised, the alignment rates were too low, about 75%. So, I want to know:
1) Why was the alignment rate (~75%) so low?
2) As for...
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