User: caggtaagtat

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caggtaagtat1.1k
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Posts by caggtaagtat

<prev • 238 results • page 1 of 24 • next >
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Answer: A: STAR index/alignment error : no exons found
... Hi, the STAR index has to be generated with a fasta file with the genomic sequence. So not just the CDNA sequences, which is used for other tools like salmon or kalisto. ...
written 21 hours ago by caggtaagtat1.1k
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Comment: C: Classic threshold for log2 fold change in RNA-seq experiment
... I would like to add, that you will have to adjust the parameter in the `results` function of DESeq2, since the default setting is, testing whether the L2FC is significantly greater or lower 0. For example: results(ds_txi, contrast=("goup", "A","B"), alpha= 0.01, lfcTreshold= 0.58) ...
written 1 day ago by caggtaagtat1.1k
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Comment: C: DESeq2 model design + contrasts (not full rank)
... I will be the only one working with the data, but I will of course document and rename the variable `flow`. The problem for correcting the bias stays the same ...
written 17 days ago by caggtaagtat1.1k
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Comment: C: DESeq2 model design + contrasts (not full rank)
... Unfortuantely, the RNA for the sample of the different flow cells was isolated on different days, so I would definitely like to correct for that bias, if possible. ...
written 18 days ago by caggtaagtat1.1k
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Comment: C: DESeq2 model design + contrasts (not full rank)
... I asked them exactly that earlier and they isolated the RNA seperately for sampes of batch A and batch B (flow). Library prep etc. was done the same for every sample. Indi is the biological individuum the samples were collected from. So ideally I would love to do `desing= flow+indi+group`. But this ...
written 18 days ago by caggtaagtat1.1k
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Comment: C: DESeq2 model design + contrasts (not full rank)
... Thank you very much for the suggestions. I know now, that all was done the same way, except of the RNA-isolation which was done seperately for samples of the different flowcells. This means, that I still have to correct for this bias, using the flowcell ID, to be absoluty correct. How would you co ...
written 18 days ago by caggtaagtat1.1k
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Comment: C: DESeq2 model design + contrasts (not full rank)
... The samples were sequenced at the same day but within other illumina flowcells. Now that you say it, the potentially batch effect seems to only affect samples of two treatments in the PCA plot. The other two treatments seem to be not affected. I will attach the figure to the question. I think this ...
written 18 days ago by caggtaagtat1.1k
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(Closed) DESeq2 model design + contrasts (not full rank)
... Hi, I have a question to the DESeq2 contrast. I have single end reads from 16 samples with 4 treatments (group) and 4 biological replicates (indi). However, the replicates are not evenly distributed across the used flowcells (flow). Can I still correct for the flowcell batch effect? My meta table ...
rank deseq2 contrast rna-seq dge written 18 days ago by caggtaagtat1.1k • updated 18 days ago by swbarnes27.9k
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Comment: C: How to remove non protein coding genes from single cell pre-mRNA seq?
... I know, but how can you only sequence pre-mRNA? Capping and poly-adenylation is happening after transcription, but splicing is already happening during transcription, so I'm genuinely curious, because I never heard of pre-mRNA seq. ...
written 4 weeks ago by caggtaagtat1.1k
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Comment: A: Genomics regions that common to atleast 10 cell types
... Maybe you could tackle this task by generating a huge bed file with all coordinates stated in your 142 bed files. And then go from there? Maybe intersecting the huge file with all 142, if thats possible? ...
written 4 weeks ago by caggtaagtat1.1k

Latest awards to caggtaagtat

Scholar 21 hours ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Guru 4 weeks ago, received more than 100 upvotes.
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Popular Question 3 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Popular Question 5 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Popular Question 5 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Scholar 6 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 8 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Scholar 8 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 9 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How to create custom gtf annotation file?
Popular Question 11 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Appreciated 12 months ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Appreciated 14 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Scholar 14 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 14 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Scholar 15 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 16 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count

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