User: zhenyisong
zhenyisong • 130
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Posts by zhenyisong
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... you can try [miniconda][1] to mange your software version. GATK4 has already lifted its restriction.
conda install -c bioconda gatk
[1]: https://conda.io/miniconda.html
[2]: https://bioconda.github.io/ ...
written 19 months ago by
zhenyisong • 130
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... Beside @Rory's suggestion, I would suggest you to pay attention to [this paper][1] (The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses) about the wet procedure. Sebastian's work argued that there were few overlaps between different pipelines.
[1]: h ...
written 21 months ago by
zhenyisong • 130
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... [iGenomes][1]. The ftp site provides the indexed human genomes for different versions.
You can also download the corresponding assembly from NCBI or ENSEMBL or UCSC.
And create your own indexed genome using
bwa index -a bwtsw
[1]: https://support.illumina.com/sequencing/sequencing_software ...
written 22 months ago by
zhenyisong • 130
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... I read the [protocol here][1]. for Ovation RNA-Seq Systems 1–16 for Model Organisms. The figure 1 at PDF page 6 said that this kit uses the first strand to construct the library. (Second Strand Synthesis with Nucleotide Analog, Ligation with Nucleotide Analog-marked Adaptors). But Please contact Nu ...
written 2.6 years ago by
zhenyisong • 130
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... I think you used the second strand to construct the library due to to the inference from the output by RSeQC. The second strand here means that the sequence order is in line with the mRNA and not the complementary DNA (cDNA). Sense-strand. If this is the case, you should use the FR. But you should c ...
written 2.6 years ago by
zhenyisong • 130
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... I installed the mirDeep2. The version is miRDeep2.0.0.8 and last modification time is 21/04/2016.
bowtie --version
#bowtie version 0.12.9
#64-bit
#Built on igm1
#Sun Dec 16 14:36:32 EST 2012
#Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-50)
#Options: -O3 -m64 -Wl ...
written 3.0 years ago by
zhenyisong • 130
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... Thanks. It is just what I mean. ...
written 3.3 years ago by
zhenyisong • 130
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Comment:
C: High-throughput sample BLAST
... @b.nota and @Farbod
Query input:
a list of genes with their expression value. (my study result from microarray or RNA-seq data)
Database:
archive all high-throughput results (microarray or RNA-seq) from various experiments
Output:
find the similar experiment in the database. I mean, I want to fi ...
written 3.3 years ago by
zhenyisong • 130
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... My aim is to use the gene profiling of my sample (RNA-seq or Microarray data) to explore the database to find the similar samples. I used my sample and public data and performed Spearman correlation, but the result has a huge batch effect.Is there any implemented solution to my problems? Thanks. ...
written 3.3 years ago by
zhenyisong • 130
• updated
3.3 years ago by
WouterDeCoster ♦ 42k
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... @cankutcubuk and @yasinkaymaz
Since the data has internally been transformed to log format, does this mean we can not analyze the data using DESeq2 or edgeR or Limma? Limma uses voom to transform the data and has a weight matrix. Other two package require count data. If I want to use these three pac ...
written 3.6 years ago by
zhenyisong • 130
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