Question: One sample pooled in a whole lane vs multiple sample in each lane
0
gravatar for bob
3.9 years ago by
bob0
Germany
bob0 wrote:

Dear All,

I have paired-end RNA-seq data sequenced using HiSeq 4000. One sample (sample#1) out of 8 samples is pooled in a whole lane and generating much more reads number for sample#1 than all other samples.

Sample1-Replicate1-Read1 - pooled in a whole lane (lane 1) - (20GB file size, 280 million reads)
Sample1-Replicate1-Read2 - pooled in a whole lane (lane 1) - (20GB file size, 280 million reads)
Sample1-Replicate2 -R1 - lane 2 - (4GB filesize, 45 million reads)
Sample1-Replicate2 -R2 - lane 2 - (4GB filesize, 45 million reads)
Sample2-Replicate1-R1 - lane 2 - (4GB filesize, 45 million reads)

Sample2-Replicate1-R2 - lane 2 - (4GB filesize, 45 million reads)
Sample2-Replicate2-R1 - lane 2 - (4GB filesize, 45 million reads)
Sample2-Replicate2-R2 - lane 2 - (4GB filesize, 45 million reads)
Sample3-Replicate1-R1 - lane 2 - (4GB filesize, 45 million reads)
Sample3-Replicate1-R2 - lane 2 - (4GB filesize, 45 million reads)
Sample3-Replicate2-R1 - lane 2 - (4GB filesize, 45 million reads)
Sample3-Replicate2-R2 - lane 2 - (4GB filesize, 45 million reads)
Sample4-Replicate1-R1 - lane 3 - (4GB filesize, 45 million reads)
Sample4-Replicate1-R2 - lane 3 - (4GB filesize, 45 million reads)
...

What is the best way to extract the read numbers from Sample1-Replicate1 (paired-end) to the level of Sample1- Replicate#2 i.e. 45 million reads out of 280 million reads file?

Many Thanks

 

 

 

 

 

 

rna-seq open • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Devon Ryan91k • written 3.9 years ago by bob0
0
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

By "extract the read numbers" I assume you mean "compensate for the difference in sequencing depth". The answer is that edgeR/DESeq2/whatever will take care of that for you.

ADD COMMENTlink written 3.9 years ago by Devon Ryan91k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1233 users visited in the last hour