Closed Hulanyue closed 4 years ago
there is a question about getting illumina paired-end reads
when I click http://eichlerlab.gs.washington.edu/pacbio-complex-regions
and get Illumina reads
about CH17-157L1,it show me You don't have permission to access /pacbio-complex-regions/illumina_reads/CH17-157L1/ on this server
.
Can you help me ?
Thank you very very much!
SRA refers to the raw reads. What you are looking for is the CH17-157L1 assembly. For this you need to search for CH17-157L1 in the NCBI nucleotide database: https://www.ncbi.nlm.nih.gov/nuccore/
then you'll get: https://www.ncbi.nlm.nih.gov/nuccore/AC254825.1
@calkan Thanks for your reply! So,the AC254825.1 is the error long read,it is okay? Can you tell me how I can get the illumina reads? Or is AC243627.3 illumina reads?(but the size of AC243627.3 is only 228k)
I am sorry ! I read the paper again and AC243627.3 is the reference genome for corrected LR. What I am looking for is the error LRs and SRs that mapped to LRs
No AC254825.1 is the assembly based on Sanger sequencing. SRR1171743 is PacBio. Illumina was available at the Eichler Lab web site, but I have no admin access to it. We also just downloaded it when it was available. Try asking John Huddleston, the first author of the related paper.
Okay,Thank you very very much! And is it https://github.com/huddlej in Github that I can ask John Huddleston?
that's him
Okay,Thank you again!
Hi,I am sorry to bother you again!
the size of CH17-157L1 data set is 231 kb in paper ,the id is SRR1171743,but the data set I download in NCBI is about 1.1G and the bases are 261.6Mbp.
I want to know whether 231kb is the size of sample when experience.
if yes,does it mean that I can sample the data from data set at will,as long as the data size(231kb) is satisfied?
Thank you!