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Search: Posts Made By: leifive
Forum: RNA Sequencing 03-27-2013, 06:44 PM
Replies: 7
Views: 4,261
Posted By leifive
Talking Thanks krespim. I have solved the problem by...

Thanks krespim. I have solved the problem by going back to Cufflinks 1.3.0, and I'm not sure whether there is a bug in the lastest version of Cufflinks or something incompatible in my reference file....
Forum: Bioinformatics 03-27-2013, 01:18 AM
Replies: 4
Views: 2,807
Posted By leifive
Hi, ccstaasts, How is your result of de novo...

Hi, ccstaasts,
How is your result of de novo using unmapped reads from tophat? I combined the pair-end and single-end unmapped reads, then assembled with CLC bio, unfortunately it returned numerous...
Forum: Bioinformatics 03-26-2013, 06:51 PM
Replies: 2
Views: 1,313
Posted By leifive
Hi, all, I got a document from , it says using...

Hi, all,
I got a document from , it says using pileup file from samtools and junctions.bed file generated by tophat with bedtools to filter SNPs, how do you think?
Forum: RNA Sequencing 03-18-2013, 06:17 PM
Replies: 7
Views: 4,261
Posted By leifive
Thanks for your reply, krespim. But I don't think...

Thanks for your reply, krespim. But I don't think this is just a bug in the reporting, because there is no "OK" status in my splicing.diff file from Cuffdiff, but NOTEST or LOWDATA instead. And I...
Forum: RNA Sequencing 03-18-2013, 07:31 AM
Replies: 7
Views: 4,261
Posted By leifive
Hi, vaibhav_jain and krespim: Have you...

Hi, vaibhav_jain and krespim:
Have you solved the problem? This has puzzled me almost one week. Why cuffdiff performed 0 splicing test?
Forum: Bioinformatics 03-18-2013, 07:18 AM
Replies: 42
Views: 20,920
Posted By leifive
Hi, fangquan. Could you tell me how you...

Hi, fangquan.
Could you tell me how you solve the problem. I am facing almost the same puzzle. I used merged.gtf from cuffmerge and combined.gtf from cuffcompare as input alternatively, but...
Forum: RNA Sequencing 03-18-2013, 02:00 AM
Replies: 0
Views: 1,548
Posted By leifive
Problem about splicing.diff from cuffdiff

Hi,
This problem has puzzled me one week long!
I followed the workflow:Tophat - Cufflinks - Cuffmerge - Cuffdiff,and everything is OK except the splicing.diff file generated by cuffdiff....
Forum: Bioinformatics 03-07-2013, 11:03 PM
Replies: 3
Views: 2,282
Posted By leifive
Oh, It's my fault. I forget to run bam2fastq with...

Oh, It's my fault. I forget to run bam2fastq with -readname option. It's OK now. Thanks again.
Forum: Bioinformatics 03-07-2013, 04:57 PM
Replies: 3
Views: 2,282
Posted By leifive
Unhappy Thanks, yzzhang. I have installed bam2fastq and...

Thanks, yzzhang. I have installed bam2fastq and running on my 500MB size unmapped.bam file. But converting it to paired end fastq files is taking much longer than the original tophat run which was...
Forum: Bioinformatics 03-07-2013, 05:15 AM
Replies: 3
Views: 2,282
Posted By leifive
Smile how to assembly unmapped reads from tophat?

Hi,
I have used Tophat/Cufflink to map and assembly my RNA-seq pair-end data(the insert size is 200bp while each read has 90bp length) with a reference genome. Now I am thinking how to de novo...
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