User: Bioinfo

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Bioinfo270
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Posts by Bioinfo

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Comment: C: Sample names for TCGA data from GDC-legacy archive
... Sure, I will be little careful from next time. thanq ...
written 15 days ago by Bioinfo270
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... I just posted the answer how I solved the problem..Yes may be I must have posted the link. I totally forgot about that while posting the solution. Sorry for that. ...
written 15 days ago by Bioinfo270
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Comment: C: Correlation between lncRNA and protein coding genes
... thanks a lot. I got the correlation coefficient values (R). This could tell whether the lncRNA has strong, moderate or weak correlation with other protein coding genes. But I have a small question what is R square in correlation? What does R square tell? ...
written 21 days ago by Bioinfo270
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Comment: C: Correlation between lncRNA and protein coding genes
... Sorry, I'm a bit confused. lets say I have matrix `A` like below. Ensembl ids as rows and Samples as columns. Using raw counts I used `cpm` function and converted them to logCPM values like below. Sample1 Sample2 Sample3 Sample4 Samp ...
written 21 days ago by Bioinfo270
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Comment: C: Correlation between lncRNA and protein coding genes
... so, with this `cor` how to proceed further? I'm interested in doing spearman correlation. ...
written 21 days ago by Bioinfo270
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Correlation between lncRNA and protein coding genes
... I have RNA-Seq data for 300 samples. In which 250 are Tumor and 50 are Normals. I have a matrix with genes as rows and samples as columns. There are almost 56k genes as rows. Among these genes there are also lncRNAs. I would like to check the correlation between a specific lncRNA and all other pr ...
R genes correlation rna-seq lncrna written 21 days ago by Bioinfo270 • updated 21 days ago by Nicolas Rosewick6.9k
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Comment: C: Is TCGA Breast cancer data strand specific?
... yes I understand with your previous comment. My question is if I have the TCGA raw sequencing data which is non-standed library protocol and if I do alignment with --rna-strandness RF (reverse forward strand specific) option will there be any problem? any effect on counts data? I'm asking this beca ...
written 4 weeks ago by Bioinfo270
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Comment: C: Is TCGA Breast cancer data strand specific?
... WHen I checked one of the sample with Rseqc I see that it is strand specific. And from this post [https://www.biostars.org/p/153627/] I see that all illumina technologies are strand specific. And if the samples are not stranded and if we do alignment with strand specific option will there be any pr ...
written 4 weeks ago by Bioinfo270
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Comment: C: Is TCGA Breast cancer data strand specific?
... that was the one I saw. The recent comment I saw for the post is non-stranded. Thats why I asked again. And I have checked the paper also there is no information about strand specific. ...
written 4 weeks ago by Bioinfo270
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Is TCGA Breast cancer data strand specific?
... Hi, I have TCGA Breast raw sequencing data fastq files. Initially with one of the sample bam file I used `Rseqc` to check whether it is strand specific or not. I see that it is Strand specific `RF` (reverse forward strandness). I have aligned all the samples with `hisat2` using the argument `--rn ...
geneexpression tcga rna-seq strand hisat2 written 4 weeks ago by Bioinfo270 • updated 4 weeks ago by genomax58k

Latest awards to Bioinfo

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 4 weeks ago, created a question with more than 1,000 views. For cuffdiff for groups
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Sample names for TCGA data from GDC-legacy archive
Student 6 weeks ago, asked a question with at least 3 up-votes. For Sample names for TCGA data from GDC-legacy archive
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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