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Forum: The Pipeline 05-28-2013, 11:25 PM
Replies: 0
Views: 4,035
Posted By huangjun
Iprscan output problem

Hi,
Everyone.
Recently, i am using iprscan to annotated my transcripts,to the ouput results, the sequence name became "Contig101107_4_ORF1" "Contig101625_1_ORF1", my input
contig names...
Forum: RNA Sequencing 10-29-2012, 03:39 AM
Replies: 0
Views: 901
Posted By huangjun
Smile RNA-seq for CNV

Hi,all,
Did anyone here used RNA-seq data for Copy Number Variation analysis?
Recently, i want to do this, but i can't choose the suitable software to do this
work, are there anyone can give...
Forum: RNA Sequencing 03-22-2012, 04:35 AM
Replies: 0
Views: 638
Posted By huangjun
Arrow Novel transcripts detecting

Hi, every body~:confused:
I have some questions about the RNA-seq analysis, First, i want to know if there have some workflows about Novel-transcripts detecting, or whether there existed some...
Forum: RNA Sequencing 02-26-2012, 10:46 PM
Replies: 0
Views: 1,110
Posted By huangjun
RNA-seq data for SNPs and Indels dissecting

Hello, everyone!
Are there anyone use RNA-seq data for snp calling and indel dissecting, i want to know which software can perform to this work. thank you !
Forum: Illumina/Solexa 02-11-2012, 08:32 PM
Replies: 7
Views: 2,871
Posted By huangjun
Hi, gringer. I want to know "make the adjustment...

Hi, gringer. I want to know "make the adjustment msnuslly" means? thank you !
Forum: Illumina/Solexa 02-08-2012, 03:55 AM
Replies: 7
Views: 2,871
Posted By huangjun
Hi, gringer, in my reads , if there have more...

Hi, gringer, in my reads , if there have more than 1 bases quality lower than 0 , or so ito large amount of reads, my be we can't know which parameter to append ?
Forum: Illumina/Solexa 02-08-2012, 03:51 AM
Replies: 7
Views: 2,871
Posted By huangjun
my data come from Illumina Hiseq 2000 ,...

my data come from Illumina Hiseq 2000 , FASTX_Toolkit can trim the low quality bases, cut off the low quality bases and mask the reads.
Forum: Illumina/Solexa 02-07-2012, 09:29 PM
Replies: 7
Views: 2,871
Posted By huangjun
Illumina sequencing Quality error

Hi, everyone!
Recently, i received the RNA-seq data, when i use FASTX_TOOKIT preprocessing the data, it shows that my data invalid, quality < 0; Is
there anyone encountered this problem...
Forum: Bioinformatics 01-05-2012, 10:17 PM
Replies: 9
Views: 4,466
Posted By huangjun
Maybe iprscan can help you, iprscan can make the...

Maybe iprscan can help you, iprscan can make the GO annotation! Or you can try the blast2go!
Forum: RNA Sequencing 12-30-2011, 09:54 PM
Replies: 3
Views: 5,751
Posted By huangjun
RPKM calculation

Hi there,
Recently, i began to learn RNA-seq analysis, to some plans, like maize, if we have the reference genome, could anyone tell me how to calculate the RPKM values? I'm thinking that...
Forum: RNA Sequencing 12-13-2011, 05:15 AM
Replies: 8
Views: 3,254
Posted By huangjun
Post RNA-seq SNP calling softwore

Hello everyone,
Recently, i began to working on RNA-seq analysis. To one species, if i have some assembled transcripts, how can i use this data to SNP calling, could you give me some...
Forum: RNA Sequencing 12-12-2011, 04:54 PM
Replies: 2
Views: 1,115
Posted By huangjun
Cool gicl error!

Hi all,
when i use gicl softwore to clustering RNA-seq de novo data, it caused errors, it showed that like follows:
gicl (allseqs.fa) encountered an error at step pairwise
...
Forum: RNA Sequencing 12-11-2011, 04:14 PM
Replies: 38
Views: 15,515
Posted By huangjun
the cufflinks only give us the rebuild assembled...

the cufflinks only give us the rebuild assembled sequence based on the reference genome, but i want to know how to get unmapped contigs also , only that we could get some new transcripts.
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