User: riccardo

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riccardo40
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Posts by riccardo

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Paired reads positions in FASTQ files
... Hi, is this also possible if you consider the original files that the sequencer gives you in output? Thanks ...
written 13 months ago by riccardo40
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Paired reads positions in FASTQ files
... Hello, I have a question about the paired end sequencing. When you have the FASTQ files of the read1 and the read2, that come from a paired sequencing, is it correct to assume that if in the position 1, of the R1 file, you have the read X in the same position of the R2 file you have the paired reads ...
sequencing written 13 months ago by riccardo40 • updated 13 months ago by genomax52k
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RSEM HTSeq unique reads
... Hi all, I have to build a STAR index with a human gene in the mouse genome and I want only the reads that map uniquely in these and other genes. Since I want also to distinguish the reads that map in these homolog genes in this case HTSeq is better than RSEM since it considers only the reads that ma ...
rna-seq written 14 months ago by riccardo40 • updated 14 months ago by h.mon16k
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Answer: A: RNA seq expression of different genes in the same sample
... Thank you very much! ...
written 16 months ago by riccardo40
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RNA seq expression of different genes in the same sample
... Hello, I would like to know if with the RNA seq you can compare the expression of different genes in the same sample. For example: SampleA GeneA 10 GeneB 5 Can I say the GeneA is expressed two times more than GeneB with a good confidence? Or is there some bias when you do this kind of comparisons ...
rna-seq written 16 months ago by riccardo40 • updated 16 months ago by huwenhuo40
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Answer: A: small RNA-seq unique reads
... Thank you! Riccardo ...
written 22 months ago by riccardo40
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small RNA-seq unique reads
... Hi, I would like to know if you use the read counts of reads that map uniquely on the genome or all the reads, unique and not, before to perform a differential expression analysis. In the case of RNA-seq it is better to consider the unique reads, as it is reported in DESeq 2 documentation. It would ...
alignment small rna-seq written 22 months ago by riccardo40
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Comment: C: PCA tpm fpkm
... Thanks for your answer. It was very clear. Normally I use DESeq2 and I can perform a PCA with rlog or VST and are very useful. Now I have used RSEM and I have TPM and FPKM and I cannot use the DESeq2 PCA because I have not integer value. If I used log2(FPKM) or log2(TPM) could I see, correctly, batc ...
written 22 months ago by riccardo40
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Answer: A: PCA tpm fpkm
... Thanks for your answer. It was very clear. Normally I use DESeq2 and I can perform a PCA with rlog or VST and are very useful. Now I have used RSEM and I have TPM and FPKM and I cannot use the DESeq2 PCA because I have not integer value. If I used log2(FPKM) or log2(TPM) could I see, correctly, batc ...
written 22 months ago by riccardo40
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PCA tpm fpkm
... Hi all, I have expression values in TPM and FPKM from RSEM. Is it correct to perform a PCA direclty on these values or I have to manipulate these values before to do the PCA? Thank you. Riccardo ...
pca fpkm tpm written 22 months ago by riccardo40 • updated 22 months ago by Ar760

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