User: TEman

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TEman10
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10
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Location:
Sweden
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1 year ago
Joined:
4 years, 7 months ago
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p******************@med.lu.se

Posts by TEman

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Sequence Bias Bismark Output Interpretation
... I am not sure if we understand each other. I have read that link. Ignore the first 10 bases. Ignore the methylation. Just look at the CHH Total Calls line. It goes from ~4,500k at the beginning to ~1000-500k at the end. What happens in between? Why are there gradually fewer total CHH calls over th ...
written 20 months ago by TEman10
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Answer: A: Sequence Bias Bismark Output Interpretation
... Thank you for your answer. I get the bias at the very start (drop of methylated C). I have already trimmed the leading bases of R2 reads. However, my concern is the gradual decrease in the CHH Total Calls and CHG Total Calls. Here is the QC from Bismark User Guide (https://rawgit.com/FelixKrueger/ ...
written 20 months ago by TEman10
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Answer: A: Sequence Bias Bismark Output Interpretation
... Hi, What about the gradual decrease in CHH total and CHG total in R2? I see the same gradual decrease over R2 in my dataset. Does anyone have an explanation for this? ...
written 20 months ago by TEman10
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STAR unique reads
... In STAR, one can use the --outFilterMultimapNmax 1 to report only reads that map exactly one time to the reference genome. This can be useful when analyzing genes and elements that have high sequence similarity. However, one thing that is unclear for me is how STAR handles reads that maps to multip ...
alignment star rna-seq written 2.2 years ago by TEman10
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R write alignment MSA
... Hi all, I read a clustal .aln file using the read.alignment function of the Seqinr package, modified the matrix, and now want to write the alignment object to a clustal .aln file format again. However, I do not find such a function. Any suggestions? ...
R alignment written 2.6 years ago by TEman10 • updated 10 months ago by Biostar ♦♦ 20
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Multiple sequence alignement MSA editing
... I want to remove all rare insertions (when it occurs in less than 5% of the sequences) in a multiple sequence alignment file (clustal .aln) with 699 sequences. That is, I have a MSA with many columns containing only one or two insertions while the rest of the sequences are blank "-". It is by far ...
R clustal alignment written 2.6 years ago by TEman10
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Detect Alternative Promoters from Single-end RNA seq
... Is there are good way of identifying alternative promoters from specific genomic locations by analyzing single-end RNA-seq data? I currently have a dataset with 50bp single end seq from Illumina HiSeq 2500. ...
rna-seq written 4.0 years ago by TEman10 • updated 4.0 years ago by harold.smith.tarheel4.5k
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CCCCCTTTTTTTTTTT reads in RNA-seq
... I have had some RNA-seq data sets (both single-end and paired-end) with (C)n(T)n sequences. E.g. 5'-CCCCCTTTTTTTTTTTTTTTTTTTTT-3' In the paired-end data set, I find this kind of sequence overrepresented in both R1 and R2. Can someone please enlighten me what this can be?   Thanks     ...
sequence rna-seq written 4.1 years ago by TEman10
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Comment: C: How to extract unique mapped results from Bowtie2 bam results?
... I don't know why I wrote that 3rd step. It is of course default behaviour in bowtie2. What I meant was to only keep an alignment if it is better than all other alignments of that read. That is, if the top alignment has the same score as the second, it should be discarded as it is "impossible" to sa ...
written 4.1 years ago by TEman10
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Comment: C: How to extract unique mapped results from Bowtie2 bam results?
... I see how this is in general a good strategy. However, when quantifying reads to repeated sequences, such as transposons, wont this cause a drastic over-estimation? If you don't extract primary or unique reads from the sam/bam, the reads that maps equally well to multiple sequences will cause a ser ...
written 4.6 years ago by TEman10 • updated 12 weeks ago by RamRS26k

Latest awards to TEman

Popular Question 18 months ago, created a question with more than 1,000 views. For GI chromosome list ncbi
Popular Question 18 months ago, created a question with more than 1,000 views. For R write alignment MSA
Popular Question 2.1 years ago, created a question with more than 1,000 views. For GI chromosome list ncbi

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