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Forum: Bioinformatics 08-07-2014, 10:24 AM
Replies: 3
Views: 1,835
Posted By shangzhong0619
Hi, dpryan. Thanks for your reply. Actually my...

Hi, dpryan. Thanks for your reply. Actually my knock out is hemizygous, so in this case, it is possible to have genes more significant than the knock out gene?
Forum: Bioinformatics 08-06-2014, 02:15 PM
Replies: 3
Views: 1,835
Posted By shangzhong0619
HTseq-count feature type choice for RNAseq

Hi all,
I am using HTseq-count to count reads in my bam files. I used ncbi mouse annotation file.
I wonder which feature type (third column of gff3 file) I should use?
My understanding of how...
Forum: Bioinformatics 07-18-2014, 12:28 PM
Replies: 36
Views: 18,490
Posted By shangzhong0619
Tophat remove rRNA reads automatically?

Hi,
I just have the opposite problem as mart555. I mapped my RNAseq to mouse gff3 file downloaded from ncbi. I didn't make any change, rRNA sequence are in the file. After mapping using tophat, I...
Forum: Bioinformatics 07-11-2014, 10:11 AM
Replies: 14
Views: 5,302
Posted By shangzhong0619
Cuffquant takes a long time

Hi all,
I have a problem about running cuffquant, when I didn't use the option '-b/--frag-bias-correct <genome.fa>', I can got results fast. However if I add that option, it always got stuck at a...
Forum: Bioinformatics 06-20-2014, 03:43 PM
Replies: 218
Views: 141,293
Posted By shangzhong0619
Thanks. It works. I have another problem, when...

Thanks. It works. I have another problem, when indexing the genome, does STAR accept gzipped fasta file? It didn't work for me and got "BUG: next index is smaller than previous", I also tried...
Forum: Bioinformatics 06-20-2014, 02:07 PM
Replies: 218
Views: 141,293
Posted By shangzhong0619
Hi Alex, Thanks for your reply, yes my...

Hi Alex,
Thanks for your reply, yes my reference fasta has many scaffolds. When I try to install the latest version, it shows the following effor.


samtools/libbam.a(bgzf.o): In function...
Forum: Bioinformatics 06-19-2014, 02:06 PM
Replies: 218
Views: 141,293
Posted By shangzhong0619
failed to generate genome using STAR

Hi, I build genome using command:
STAR --runMode genomeGenerate --genomeDir STAR_pathway --genomeFastaFiles file.fa.gz --runThreadN 10
Then I failed and got message: "BUG: next index is smaller...
Forum: RNA Sequencing 06-15-2014, 10:55 PM
Replies: 4
Views: 6,142
Posted By shangzhong0619
Hi Robby. Thanks for your reply. So for example...

Hi Robby. Thanks for your reply. So for example if I have paired end RNA seq. All reads in the first fastq file are forward reads, all reads in second fastq file are reverse reads. Then if I map...
Forum: RNA Sequencing 06-15-2014, 10:10 PM
Replies: 4
Views: 6,142
Posted By shangzhong0619
Does Strand-specific RNA-seq mean reads from one genome strand?

Hi all,
I got a little bit confused about the strand specific RNA-seq. I saw the dUTP protocol to generate strand specific RNA seq, it seems that it amplifies the sequence which is complement to...
Forum: Bioinformatics 05-26-2014, 02:18 AM
Replies: 12
Views: 6,791
Posted By shangzhong0619
Hello, GenoMax, I have a question, there are 16...

Hello, GenoMax, I have a question, there are 16 nr files in the ftp, can I use cat to concatenate the files with the same extension in those 16 folders and finally get only one big database? I don't...
Forum: Bioinformatics 05-25-2014, 10:52 PM
Replies: 12
Views: 6,791
Posted By shangzhong0619
Hi, just a question, how many transcripts did you...

Hi, just a question, how many transcripts did you search using -remote? how is the speed? thanks.
Forum: Bioinformatics 04-13-2014, 11:33 PM
Replies: 189
Views: 71,489
Posted By shangzhong0619
How does sliding window work

I was just wondering how does sliding window in trimmomatic work?
The definition is scanning from the 5 end of the read, and removes the 3
end of the read when the average quality of a group of...
Forum: Illumina/Solexa 04-06-2014, 01:37 PM
Replies: 15
Views: 12,323
Posted By shangzhong0619
Thank you very much Brian. I don't know how to...

Thank you very much Brian. I don't know how to paste the figure. I post in the attachment. 2967.
According what you said, we should trim the adapters for each sample we analyze? But I only have...
Forum: Illumina/Solexa 04-06-2014, 12:22 PM
Replies: 15
Views: 12,323
Posted By shangzhong0619
thanks for your reply. Sorry, it is adapter...

thanks for your reply. Sorry, it is adapter removal function. Still have some questions.
1. What does insert mean? index reads barcodes?
2. My samples are already de-multiplexed and I didn't find...
Forum: Illumina/Solexa 04-06-2014, 11:39 AM
Replies: 15
Views: 12,323
Posted By shangzhong0619
Do illumina fastq file have barcode and adaptor?

Hi all,
I saw this thread http://seqanswers.com/forums/showthread.php?t=8176. It said that in illumina fastq file, there is no barcode. But when I see the manual of trimmomatic, why is there a...
Forum: Bioinformatics 01-20-2014, 02:24 AM
Replies: 4
Views: 1,602
Posted By shangzhong0619
Hi Devon, what about finding SNPs? Is it useful...

Hi Devon,
what about finding SNPs? Is it useful to include those orphaned reads when finding SNPs?
Forum: Bioinformatics 01-19-2014, 11:20 PM
Replies: 4
Views: 1,602
Posted By shangzhong0619
How to deal with paired end reads with one mapped, the other not

Hi all,
I am using gsnap to map paired end reads to reference, and got sam file as output. However, it seems that in the file, there are some pairs with only one end mapped to the reference, the...
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