User: elsoja

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elsoja30
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Posts by elsoja

<prev • 22 results • page 2 of 3 • next >
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Comment: C: Transcripts with beta close to zero are considered differentially expressed in a
... They don't ![enter image description here][1] [1]:http://i.imgur.com/nawM1Sa.png ...
written 21 months ago by elsoja30
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Comment: C: Transcripts with beta close to zero are considered differentially expressed in a
... It's a simple design with just one condition: Tissue A (6 samples) vs. Tissue B (3 samples) ...
written 21 months ago by elsoja30
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Transcripts with beta close to zero are considered differentially expressed in a likelihood-ratio test in sleuth
... I'm comparing the results that I obtain when doing a DE analysis with the Wald test and the likelihood-ratio test. One the thing that I've noticed is that there are many genes with 'beta' close to zero that are considered differentially expressed between the conditions. I know that the likelihood-r ...
sleuth differential-expression rna-seq written 21 months ago by elsoja30
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DE analysis of low-expression transcripts
... I'm working with lncRNAs, which have very low expression levels, and I'm not sure if I can conduct a standard DE analysis with them. Does packages like DESeq2, edgeR or sleuth work well with low expression transcripts? If not, how should I proceed? ...
sleuth expression deseq2 rna-seq edger written 2.4 years ago by elsoja30 • updated 2.4 years ago by Devon Ryan90k
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How to create 'gene' and 'transcript' entries in a GTF containing only exons
... The result of Cufflinks is a GTF file that only has exons. I need to create a new GTF that includes 'gene' and 'transcript' entries. Is there a automated way to do that? **Example:** FROM: chr1 Cufflinks exon 4807788 4807982 . + . gene_id "XLOC_000019"; transcrip ...
gtf cufflinks written 2.5 years ago by elsoja30 • updated 23 months ago by gandrescabrera80
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Using Stitch MAF blocks withou Galaxy
... I want to prepare some alignments to use as input in PhyloCSF (using the mouse multiz60way alignments and a GTF file) but I can't run the 'Stitch MAF blocks' script in Galaxy. I can't install it in our local server and the remote server (usegalaxy.org) doesn't finish the job. Is there a way of runn ...
maf stitch galaxy written 2.5 years ago by elsoja30
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Comment: C: Cufflinks displaying "WARNING: Multi-Hit not found"
... I ran cuuflinks without the '-u' option ...
written 2.5 years ago by elsoja30
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Cufflinks displaying "WARNING: Multi-Hit not found"
... I'm running Cufflinks (2.2.1) on a set of RNA-seq alignments that I did with STAR. I'm using these options: /home/user1/Data/Softwares/cufflinks-2.2.1/cufflinks -p 6 -u -o ./Cufflinks/ERR036348_pass-2 ./Alignments/ERR036348_pass-2/ERR036348_pass-2_Aligned.sortedByCoord.out.bam In every instanc ...
warning multi-hit rna-seq cufflinks written 3.0 years ago by elsoja30
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Comment: C: Transforming stranded RNA-Seq libraries in unstranded
... I'm filtering for lincRNAs in both libraries and them I'll check differential expression for each lincRNA. ...
written 3.1 years ago by elsoja30
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Transforming stranded RNA-Seq libraries in unstranded
... I want to detect differential gene expression by comparing two different RNA-Seq libraries, however one of them is stranded and the other one is unstranded. I know that unstranded libraries overrate the expression of RNAs that have a anti-sense transcript. In order to eliminate this bias, can I ali ...
rna-seq stranded written 3.1 years ago by elsoja30 • updated 10 months ago by Biostar ♦♦ 20

Latest awards to elsoja

Popular Question 12 months ago, created a question with more than 1,000 views. For Microbial diversity analysis using whole-genome metagenomic data
Popular Question 20 months ago, created a question with more than 1,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 20 months ago, created a question with more than 1,000 views. For Insert size in RNA-Seq library

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