SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 16 of 16
Search took 0.00 seconds.
Search: Posts Made By: Pengfei Liu
Forum: Bioinformatics 02-19-2014, 04:17 AM
Replies: 0
Views: 1,221
Posted By Pengfei Liu
Antisense RNA analysis from strand specific RNA-seq

Dear all

I am working on 12 samples of strand specific bacterial RNA-seq data(4 reps for 3 treatment). I have finished the DE analysis by using BWA-MEM for mapping, HTSeq for read count...
Forum: Bioinformatics 11-07-2013, 05:12 PM
Replies: 0
Views: 1,304
Posted By Pengfei Liu
How to get the Gene names to GO terms for bacteria and archaea

Hi,
I want to use goseq to do GO enrichment of RNAseq data of a bacteria and archaea. But I was stucked by the gene to GO term list.
I have try the biomart method...
Forum: Bioinformatics 10-04-2013, 04:20 AM
Replies: 6
Views: 11,346
Posted By Pengfei Liu
Sorry, I use bwa-mem to do alignment. I have...

Sorry, I use bwa-mem to do alignment. I have tested, in that, -a , -M will affect the output. -a will produce all alignment (so, secondary alignment with 0x100 will appear), and chimeric alignment...
Forum: Bioinformatics 09-15-2013, 10:40 PM
Replies: 6
Views: 11,346
Posted By Pengfei Liu
2 In the bwa-mem document, what does unpaired...

2 In the bwa-mem document, what does unpaired paired-end reads mean(-a parameter description)? what is the differences between it and singleton?

3, does the chimeric alignment get a mapping...
Forum: Bioinformatics 09-15-2013, 10:36 PM
Replies: 6
Views: 11,346
Posted By Pengfei Liu
Thanks so still some additional questions 1,...

Thanks
so still some additional questions
1, I want to use the mapping results of bwa to do Differential expression analysis, what kind of reads should be kept?
1) mapping quality q>threshold(30...
Forum: Bioinformatics 08-28-2013, 01:10 AM
Replies: 6
Views: 11,346
Posted By Pengfei Liu
Post how many mismatches does BWA-MEM tolerate during mapping

Hi,
Recently I am trying to use BWA-MEM to do alignment on PE-90 reads, I have some questiones list as following;


1,how many mismatches does BWA-MEM tolerate during mapping?
Does the...
Forum: Bioinformatics 08-24-2013, 06:26 PM
Replies: 2
Views: 1,983
Posted By Pengfei Liu
Thanks for your reply!

Thanks for your reply!
Forum: Bioinformatics 08-22-2013, 06:25 PM
Replies: 2
Views: 1,983
Posted By Pengfei Liu
Question why the properly paired results from bwa mem is an odd number

Hi
following is the results of samtools flagstat results. I use bwa mem default command to do align! my question is why the properly paired is odd number?

25700926 mapped

25744459 + paired in...
Forum: RNA Sequencing 07-07-2013, 07:12 PM
Replies: 0
Views: 1,606
Posted By Pengfei Liu
Question analysis of TSS by RNA-seq

Hi,
In order to identify the TSS of bacteria by RNA-seq, is strand specific RNA-seq enough? Or some other special :confused:kind library construction methods needed?

Thanks!
Forum: RNA Sequencing 05-21-2013, 12:11 AM
Replies: 1
Views: 1,011
Posted By Pengfei Liu
standard of clean data

Hi all
I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as following:
1. remove reads with adaptors
2....
Forum: RNA Sequencing 05-07-2013, 06:56 PM
Replies: 2
Views: 1,324
Posted By Pengfei Liu
Do you have any idea on this issue now? I am also...

Do you have any idea on this issue now? I am also concerned with this problem.
Forum: Illumina/Solexa 03-12-2013, 12:31 AM
Replies: 1
Views: 1,495
Posted By Pengfei Liu
Same question. I asked the technian of BGI, They...

Same question. I asked the technian of BGI, They gave me similar answers.
Forum: RNA Sequencing 02-19-2013, 09:46 PM
Replies: 0
Views: 1,003
Posted By Pengfei Liu
Question RNA quality of my samples, what to do next?

Recently I am working on the transcriptome of Methanocella conradii HZ254 (a methanogenic archaea isolated in our lab)
I have three culture systems:
1), HZ254 pure culture,
2), P....
Forum: RNA Sequencing 01-13-2013, 06:20 PM
Replies: 0
Views: 1,715
Posted By Pengfei Liu
Question RIN of bacteria and archaea

Hi,
I am going to run a RNA-seq of prokaryotes (a bacteria strain, an archaea strain and the combination of the two). Now I am confused about the RIN number of the prokaryotes. Form reading paper...
Forum: RNA Sequencing 01-10-2013, 06:28 PM
Replies: 1
Views: 3,287
Posted By Pengfei Liu
Unhappy one lane or two lane in RNA-seq

hi all,
I have RNA-seq project with 3 treatment and 4 replicates per treat, my supervisor want me to use MiSeq. But i find Miseq only get 7.5-8.0G data per lane, so I have to use run on two...
Forum: Illumina/Solexa 01-07-2013, 04:36 AM
Replies: 0
Views: 1,182
Posted By Pengfei Liu
basic cost for RNA-seq by Hiseq 2000

Hi,
I am going to do a RNA-seq,I want to know how much will it cost for 1 Gb data, from the library prep to finally get the data,thanks!
Showing results 1 to 16 of 16

 


All times are GMT -8. The time now is 04:52 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO