User: caggtaagtat

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caggtaagtat200
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Posts by caggtaagtat

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Answer: A: Only 1% of reads are used as "input reads" in STAR
... Ok I learned, that in fact my FASTQ files was corrupt after using sortMeRNA to remove reads from rRNA It seems like there can be an error during the run, where it inserts a blank line in your FASTQ file, which leads to STAR cutting the whole file at that position. I hope after removing of the line ...
written 5 days ago by caggtaagtat200
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Comment: C: How to repair corrupted fastq files after sortmeRNA
... Thank you so much! I had the same problem and found the blank line exactly were STAR couldn't proceed. Interestingly, on the other hand, salmon had no problems with that blank line whatsoever Thanks again for pointing out what to look for. I will have to implement a control for this error in my wo ...
written 5 days ago by caggtaagtat200
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Answer: A: Question about analysis design in DeSeq2
... I think you could also use something like this in your design parameter of the DESeq function design = ~ Disease + Treatment + Individuum and then you could check if there are big differences in your result tables with and without takeing into account the individuum. ...
written 8 days ago by caggtaagtat200
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Comment: C: Only 1% of reads are used as "input reads" in STAR
... I will try that, thank you. ...
written 8 days ago by caggtaagtat200
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Comment: C: Only 1% of reads are used as "input reads" in STAR
... Mapping with salmon worked and I don't see any errors during trimming Edit: with salmon 330 million rads were mapped ...
written 8 days ago by caggtaagtat200
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Comment: C: Only 1% of reads are used as "input reads" in STAR
... Oh your right, I edited it in the question ...
written 8 days ago by caggtaagtat200
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Only 1% of reads are used as "input reads" in STAR
... Hi everybody, I just did the alignment of my samples and for one of the samples, STAR used only 1% of the reads of the trimmed fastq file for mapping. Does someone know, what the reason could be for that? The references I used worked just fine for the rest of the data and I ran out of ideas where t ...
mapping star input rna-seq written 9 days ago by caggtaagtat200
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Comment: C: Calculating fpkm from raw counts
... Ok, so for manually comparing expression of the same genes within the same organism, I would always use TPM. However, I never did this manually, but always with the DESeq2 package of R since it does the normalization for you and comes with various additonal features. Therefore, I would definitively ...
written 21 days ago by caggtaagtat200
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Answer: A: Calculating fpkm from rraw counts
... Hi vina, [This][1] is a quiet helpful article about normalized counts. According to it, FPKM are calcualted like this: > These three metrics attempt to normalize for sequencing depth and > gene length. Here’s how you do it for RPKM (or FPKM): > > 1)Count up the total reads in a ...
written 23 days ago by caggtaagtat200
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Comment: C: Trimming RNA-Seq Data
... > Would trimming maybe 7 bases from the start of the reads and maybe 3 bases at the end help with the per base sequencing content? I just wanted to add, that like genomax said, although the distribution looks a little more extreme than usuall RNAseq data, it is characteristic for e.g. Illumina R ...
written 4 weeks ago by caggtaagtat200

Latest awards to caggtaagtat

Scholar 5 days ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Supporter 9 weeks ago, voted at least 25 times.
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Appreciated 3 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?

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