User: caggtaagtat

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caggtaagtat470
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Posts by caggtaagtat

<prev • 164 results • page 1 of 17 • next >
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Comment: C: Suggestions for Trimmomatic and "illuminaclip" parameter
... Ok, so I personally would use the `SLIDINGWINDOW:5:20` parameter since it results in a more precise clipping of bases which were called with low quality. In this case, it slides over the sequences beginning at the 5'end and looks at a window of 5 bases. If the average phred score is lower 20, it cut ...
written 22 days ago by caggtaagtat470
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Answer: A: Suggestions for Trimmomatic and "illuminaclip" parameter
... Hi, I always use trimmomatic, since it already has the adapter sequences of differnt Illumina systems stored internally. Trimmomatic executes the parameters in the order they are stated, so I first use the `ILLUMINACLIP:TruSeq3-SE:2:30:10` parameter to remove any remaining adapters than I use the ...
written 23 days ago by caggtaagtat470
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Answer: A: Enrichment Analysis with only GeneSymbols
... I just used [Agrigo][1], which is also suiteable for human an mouse genes. You have to convert the gene IDs to MGI IDs though, for example with the help of the biomart of ensembl. It than gives you the GO-terms plus the p-value for their enrichment test. This table can then be used for condensing t ...
written 24 days ago by caggtaagtat470
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Comment: C: Splice site usage from RNA-seq data
... In addition to that, if you are interested in such things, you can also look at the coverage of exon junctions, using R packages like for example "spliceSites". ...
written 4 weeks ago by caggtaagtat470
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Answer: A: Pathway enrichment and analysis of mice gene sets in R platform
... Hi, I like the EGESA package, which combines a set of already existing tools, into one output. ...
written 6 weeks ago by caggtaagtat470
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... I used `samtools view` to get the reads which overlap with my region of interest, but I then had to crop the sequences within the bam files, so that I always get the variation of the epitop of interrest within the reads. At the end, I used `sam2pairwise`, as cmdcolin suggested, and used the annotati ...
written 6 weeks ago by caggtaagtat470
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... Ok, I will have to do it manually then by counting all mapped nucleotides from the first mapped position, I guess. ...
written 6 weeks ago by caggtaagtat470
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... Thank you! Slicing the bam files by genomic coordinates is exactly what I want at the end. I will give sambamba slice a try. I just tested it again and apparently, when using `samtools view file.bam "chr:630-640"` gives me all reads which somehow overlap with the region. Some reads start at position ...
written 6 weeks ago by caggtaagtat470
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... Ah ok thanks, the reads with deletions confused me, since they start somewhere completely different but overlap my region with a deletion. ...
written 6 weeks ago by caggtaagtat470
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Comment: C: Extract read sequence from BAM files depending on the alignment coordinates
... Thank you, I can definitly work with that. Would the `samtools view file.bam reference:630-640` lead to reads which only start within the region? Or does it also ouput reads starting, for example at 600 and endong at 650? I used it on my data, but was not sure if the output is correct ...
written 6 weeks ago by caggtaagtat470

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Popular Question 20 days ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 22 days ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Popular Question 3 months ago, created a question with more than 1,000 views. For STAR do i need --twopassMode ?
Scholar 5 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
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?
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Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Scholar 10 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
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