User: Xin

gravatar for Xin
Xin60
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60
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1 year, 6 months ago
Joined:
3 years, 10 months ago
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Posts by Xin

<prev • 14 results • page 1 of 2 • next >
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(Closed) Duplicated Gene ID in gene_exp.diff file
... Hello I have run Cufflinks suit to get differentially expressed genes. I used annotation file for this analysis. In "gene_exp.diff" file I have found a duplicated gene id (HORVU1Hr1G021800 : It is for barley) with same location but different FPKM values. How can I interpret such issue? Any h ...
rna-seq written 18 months ago by Xin60 • updated 17 months ago by Biostar ♦♦ 20
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miRNA analysis by miRDeep2
... Hey guys, I would like to analyze a set of miRNA data by suing miRDeep2. I have three samples and each has two replicates. I managed to find out novel and known miRNAs by using config.txt in mapper.pl command line like this: mapper.pl config.txt -d -c -i -j -l 18 -m -p genome_index -s reads.fa - ...
mirdeep2 mirna written 2.0 years ago by Xin60
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VelvetOptimiser can't go further
... Dear all, I used Trinity to assemble my reads before. Now I'd like to assemble those reads with another tools such as Velvet/Oases. I tried to use VelvetOptimiser to find out optimized kmer and other parameters. But every time I run the program It stops in a specific line. It does not give any err ...
rna-seq written 2.3 years ago by Xin60
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Answer: A: Genome assembly tools
... I am not familiar with MIRA. I use Trinity for De-novo assembly (Initial assembly). After that, I use Cap3 to remove redundant sequences and build a meta-assembly. I think these two tools are good. ...
written 3.2 years ago by Xin60
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Normalization in RNA-seq
... Hiii dear friends..  I used TopHat and CUfflinks suite applications to find out differential expression.  I just followed the QC -> TopHat -> Cufflinks -> Cuffmerge -> Cuffdiff -> Cummerbund Then my boss asked me: " Did you do normalization?! "; "Did you use any t-test or Baysian o ...
rna-seq written 3.8 years ago by Xin60 • updated 3.8 years ago by kanwarjag980
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Comment: C: prep_reads.info vs. align_summary.txt
... I seeeeeee. I did not know thaaat. I thought we can eliminate short reads only by trimmomatic (MINLEN). I did not know mapping tools also eliminate some reads. Like alwaaays, thank youuuuuuu Devon~~ ...
written 3.8 years ago by Xin60
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prep_reads.info vs. align_summary.txt
...   ~~Hii~~ I used TopHat to map my reads against their relative reference genome. When I look inside prep_reads.info, I see: left_min_read_len=90 left_max_read_len=90 left_reads_in =24995053 left_reads_out=24994132 right_min_read_len=90 right_max_read_len=90 right_reads_in =24995053 rig ...
tophat rna-seq written 3.8 years ago by Xin60 • updated 3.2 years ago by Biostar ♦♦ 20
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Comment: C: transcripts.gtf files size vs. merged.gtf
... I seeeeeeee. Thank youuuuuu veryyy much. ...
written 3.8 years ago by Xin60
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transcripts.gtf files size vs. merged.gtf
... Hiii~~ I have two transctipts.gtf files which are outputs of cufflinks. One is 69.4 Mb and the other one is 38 Mb. When I merge these files with their annotation file the merged.gtf file is 75 Mb. Why it is small in size? (69.4 + 38 = 107.4), so I mean the minimum size of merged file should be 107 ...
rna-seq written 3.8 years ago by Xin60
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Cufflinks bias correction
... Hi all My boss asked me to do correction for my data generated from cuffdiff to eliminate bias. When I was doing cuffdiff, I wrote  -b <genome.>  in my cuffdiff command line. As I know it also does bias correction. Then I told my boss, cufflinks does correction. He asked me, what kind of te ...
rna-seq written 3.9 years ago by Xin60 • updated 2.6 years ago by Biostar ♦♦ 20

Latest awards to Xin

Popular Question 2.0 years ago, created a question with more than 1,000 views. For Normalization in RNA-seq
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Cufflinks bias correction
Popular Question 2.6 years ago, created a question with more than 1,000 views. For GC content and Kmer
Popular Question 3.2 years ago, created a question with more than 1,000 views. For GC content and Kmer
Autobiographer 3.9 years ago, has more than 80 characters in the information field of the user's profile.

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