User: realnewbie

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realnewbie10
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Posts by realnewbie

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... The code above was working two days ago, but did not work yesterday. Here is the thing, I guess, one of the packages I have downloaded before GenomicFeatures prevented the code above to work properly (although there were no warning, package masking). Where do I know this from? Simple, today the co ...
written 8 days ago by realnewbie10
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... Using the code above For zebrafish, what you can do is: #first get the gtf file from, lets say, ensembl library(GenomicFeatures) #the function above makeTranscriptDbFromGFF is now have different name, make sure that you type the correct one txdb <- makeTxDbFromGFF("Danio_rerio.GR ...
written 10 days ago by realnewbie10
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Comment: C: How to (and where) download Zebrafish Reference Genome (other than Ensembl or US
... I got my mistake. As it was stated on the [Intro2RNASeq][1] as "UCSC and Ensembl differ in their naming conventions and the frequency of updates", it is important to use same files from same browser and so on. It is also possible to download recent zebrafish genome assembly and annotation files from ...
written 3 months ago by realnewbie10
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How to (and where) download Zebrafish Reference Genome (other than Ensembl or USCS)?
... Hi, I need to downlaod a reference genome file for zebrafish genome. I have tried the recent assembly (GRCz11) from Ensembl and USCS (in compressed file format, fa.gz). The thing is the file I have downloaded from USCS did not work in STAR Aligner. In addition, there is no such file in Ensembl incl ...
genome fasta zebrafish reference daniorerio written 3 months ago by realnewbie10 • updated 3 months ago by WouterDeCoster35k
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Comment: C: Changes log2FC values of DESeq2
... before baseMean log2FoldChange lfcSE stat pvalue padj ENSDARG00000000001 139.799933351948 0.058625459923395 0.17453323038766 0.335898555210265 0.736947366599281 0.999878824603975 ENSDARG00000000002 532.33641136017 0.065047467376644 0.139490979480544 0.466320242490779 0.640986291495346 0.9998 ...
written 11 months ago by realnewbie10
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Changes log2FC values of DESeq2
... Hi, I've used DESeq2 package to analyze DEGs of my RNA-seq data, (I guess) 4 months ago, and now I wanted to double check the results by re-analyzing the data. Although baseMean values are exactly the same, log2fc, lfcse,stat,pvlaue values have sligtly changed. What could be the reason behind it? ...
#log2fc #changedstatistics #deseq2 written 11 months ago by realnewbie10
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Answer: A: how to fix Kmer count from FastQC?
... Is it because of adapter content? If it is so, there are some tools that might help you in the adapter trimming process. ...
written 12 months ago by realnewbie10
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Comment: C: NextSeq 500 RNA-Seq results
... You are god damn right :) Actually, I am trying very hard. I did not take any course that teaches RNA-seq data analysis from scratch. I am trying to understand and learn every detail in a very short period of time . To combine all the details together and produce something meaningful and right could ...
written 12 months ago by realnewbie10
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Comment: C: Multiple Conditions Testing in DESeq2 with unequal number of replicates
... Yes,you are right. Thanks for your time. However, I was wrong. Sorry for misleading to you. Each treatment is different from each other (but the .1 or.2 meaning relicas for same treatment conditions from different wells),so each control of each treatment is also different(i.e: targeting vector vs em ...
written 12 months ago by realnewbie10
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Comment: C: Multiple Conditions Testing in DESeq2 with unequal number of replicates
... same cell lines with same treatment, but from different wells. ...
written 12 months ago by realnewbie10

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Popular Question 9 months ago, created a question with more than 1,000 views. For TCGA data(RPKM) differential gene expression

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