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Forum: Epigenetics 05-10-2016, 08:36 AM
Replies: 4
Views: 2,580
Posted By liaojinyue
How to estimate representation of RRBS library

Dear all,

We have recently generated RRBS libraries and sequenced them. Although the CpG site coverage is acceptable (~1M with coverage > 10), we are puzzled by the alignment result. Enclosed...
Forum: Sample Prep / Library Generation 10-24-2014, 07:12 AM
Replies: 270
Views: 104,047
Posted By liaojinyue
data analysis

Hi Simone,

We have just received the sequencing result using smart-seq2. The input material for each sample is 10 cells and we got around 10M PE100 reads for each sample. We then tried to analysis...
Forum: Bioinformatics 07-25-2014, 07:57 AM
Replies: 191
Views: 62,820
Posted By liaojinyue
Error: 'pair_alignments' needs a sequence of paired-end alignments

Hi Simon,

I'm new to HTSeq and encountered an error when analyzing our stranded paired-end RNA-seq data.

Let me describe the procedure of my analysis.
1. Use cutadapt to trim adapters and trim...
Forum: Sample Prep / Library Generation 07-25-2014, 07:36 AM
Replies: 1
Views: 827
Posted By liaojinyue
Big variation of output for individual library

Hello all,

We recently received our RNA-seq data from the vendor. We sequenced 8 libraries as a pool and we were supposed to get around 30M reads for each sample. After reviewing the data, we saw...
Forum: Bioinformatics 07-16-2014, 03:15 AM
Replies: 1
Views: 1,175
Posted By liaojinyue
interpretation of fastQC result

Dear All,

I'm just got my RNA-seq result back but I'm new to analysis. I decided to try it out following the tuxedo protocol. After alignment with Tophat2 following quality trimming, I got...
Forum: Sample Prep / Library Generation 05-18-2014, 10:45 PM
Replies: 270
Views: 104,047
Posted By liaojinyue
strange cDNA profile after SMART-Seq2

Hi, Simone, we are testing SMART-seq2 protocol in our lab recently. It's quite impressive in terms of cDNA yield after preamplification. However, we notice that the our cDNA library is not as uniform...
Forum: Sample Prep / Library Generation 03-17-2014, 12:57 AM
Replies: 270
Views: 104,047
Posted By liaojinyue
We are buying reagents for smart-seq2. It turns...

We are buying reagents for smart-seq2. It turns out that TSO is not very cheap(~750usd for the smallest scale 250nmole)? Meanwhile I want to make sure there is nothing wrong with my technique...
Forum: Sample Prep / Library Generation 03-16-2014, 09:17 PM
Replies: 270
Views: 104,047
Posted By liaojinyue
Hi, daantje, have you figured out the cause of...

Hi, daantje, have you figured out the cause of low yield? I tried the kit recently and also encountered similar problem, only got less than 1ng amplified cDNA from 500pg input RNA provided in the kit...
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