User: SMILE

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SMILE50
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Posts by SMILE

<prev • 32 results • page 1 of 4 • next >
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Is Kallisto Sleuth pipeline suitable for all organisms?
... Hi all, I prefer to use Kallisto-Sleuth pipeline to do differential gene expression analysis now. But there is one thing I am not sure, is Kallisto Sleuth pipeline also work well for organisms which have incomplete annotation such as chicken, quail, sheep etc. Since Kallisto use transcriptome refe ...
sleuth kallisto rna-seq written 7 weeks ago by SMILE50
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what is the corresponding proteome or transcriptome (cDNA fasta in Ensembl) file in NCBI?
... Hi all, I am using Kallisto to quantify the transcript expression. I will use the transcriptome reference file (cDNA fasta) as a reference. I know we could download cDNA file directly in Fasta format from the Ensembl FTP site > wget > ftp://ftp.ensembl.org/pub/release-92/fasta/ovis_aries/c ...
assembly quantification kallisto rna-seq index written 7 weeks ago by SMILE50
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Comment: C: How to repair corrupted fastq files after sortmeRNA
... Can you explain how your tool will repair the corrupted fastq files? The original files were not corrupted. Some thing went wrong when I do sortmerna and unmerge-paired-reads.sh to get the paired files, they have different number of lines(210133674 S3-sortmerna_1.fq 210133672 S3-sortmerna_2.fq) ...
written 4 months ago by SMILE50
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How to repair corrupted fastq files after sortmeRNA
... Hi all, After removing rRNA in the fastq files with sortmeRNA, one of the paied reads was corrupetd, which failed to do fastqc with error: uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile. ...
software error alignment rna-seq written 4 months ago by SMILE50 • updated 9 weeks ago by matt.shenton40
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Strange distribution of logFC
... Dear all, I have RNAseq data of two groups. After doing differential gene expression using edgeR and DESeq2(the results are similar). I found the distribution of logFC is a little strange, having two peaks in the distribution. My guess would be that most genes are equally enriched in both goups, i ...
differential expressed genes rna-seq edger written 8 months ago by SMILE50 • updated 8 months ago by Devon Ryan81k
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... I am not sure "RNA is composed of exons" is true after reading [this paper][1]. I don't want to be rude. I just want to know whether my understanding is right. [1]: https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-8-149 ...
written 9 months ago by SMILE50
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... I don't agree with what you said about differntial isform/CDS usage. Differential isoform expression (DIE) and differential isoform usage (DIU) are related but distinct concepts. DIE assesses the difference of absolute expression in isoform level. In contrast, DIU assesses the difference of relative ...
written 9 months ago by SMILE50
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... Sorry about the misunderstanding caused by my poor English, I am not meaning bad. What I mean when I say biology is too complex, is that when we analyze some biology problems, sometimes we have to do some compromise. For example, when we talk about measuring gene expression level, it is based on t ...
written 9 months ago by SMILE50
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... The biology is too complex... I know that the eukaryotic genomes are pervasively transcribed, and that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and many biological processes utilize and require noncoding RNAs. But when we talk about ...
written 9 months ago by SMILE50
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Comment: C: Differential gene expression based on "exon" or "CDS"?
... Since in the annotation gtf file I see "exon" and "CDS". I thought edfferential expressed gene analysis could be based on CDS, which is more meaningful in my understanding ...
written 9 months ago by SMILE50

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