User: caggtaagtat

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caggtaagtat390
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Posts by caggtaagtat

<prev • 153 results • page 1 of 16 • next >
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Comment: C: Transcript assembly with nanopore long reads
... Ok thanks, I din't even think about publicly availible short read data. But since the particular strain is also annotated in ensembl there might be some data out there ...
written 7 days ago by caggtaagtat390
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Comment: C: Transcript assembly with nanopore long reads
... I'm working with HCMV which is around 230 kb long. Thanks, I will try to convinve my colleague, to add some short read data. I am more familier with those and will then give FMLRC a try. ...
written 7 days ago by caggtaagtat390
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Transcript assembly with nanopore long reads
... Hi, I'm looking for transcripts in an poorly annotated retrovirus, using oxfort nanopore reads. Currently, I'm trying to first "correct" the trimmend read sequences with the software `canu` and plan to do the assembly using the `PASA pipeline` (which uses the `trinity` module). I'm completly new t ...
assembly long reads transcriptome written 7 days ago by caggtaagtat390 • updated 7 days ago by colindaven950
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Comment: C: Differential expression comparing two groups normalized to a third group
... How exactly do you want to normalized the expression? If the normalization factor would be the same for a gene of group 2 and group 3 it wouldn't make a difference, would it? Would it may be sufficient to do differential gene expression analysis with e.g. DESeq2 between group 1 and group 2 and also ...
written 11 days ago by caggtaagtat390
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Comment: C: RNA seq stranded
... So you mean, how the reverse stranded sequences are removed after cluster generation through amplification of a single sequence? So I'm only am familiar with Illumina a bit and I don't know exactly how it works, but there are two kinds of adapters at the ends of these amplified cDNA sequences, which ...
written 11 days ago by caggtaagtat390
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Answer: A: RNA seq stranded
... Hi there, the word "stranded" refers not to the coding direction of the gtf file, but wether the obtained reads are either complementary or equal to the sequence of the sequenced fragment. In other words: first you have fragmented RNA which is used for the library preparation. During this prepara ...
written 11 days ago by caggtaagtat390
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Comment: C: Where can I find the reference files for the 1000 Genome project VCF data?
... Ok thank you. So I will download the GRCh37 annotation then. ...
written 12 days ago by caggtaagtat390
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Where can I find the reference files for the 1000 Genome project VCF data?
... Hello, I just started working with VCF files and would like to use the data of the 1000 Genome project. I found that the most recent version can be downloaded at ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . For my functional analysis, I need the position of every exon borders. There ...
vcf 1000 genome reference written 12 days ago by caggtaagtat390 • updated 12 days ago by finswimmer9.0k
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Comment: C: Haplotype annotation in VCF file of phase 3 1000 Genome project
... Thank you very much! That helps a lot. So when I'm looking for SNPs which can occur homozygous, I would check for at least one entry with `n|n` or `n/n` with n > 0 ? ...
written 18 days ago by caggtaagtat390
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Haplotype annotation in VCF file of phase 3 1000 Genome project
... Hi there, I'm new to vcf file analysis and would like to download a huge database for human SNPs with information about the location, sequence variation and if it is possible to be homozygous. So far I found this directory for files of the [1000 genome project][1] where I think I can download the ...
vcf haplotype snp written 18 days ago by caggtaagtat390 • updated 18 days ago by finswimmer9.0k

Latest awards to caggtaagtat

Popular Question 7 weeks ago, created a question with more than 1,000 views. For STAR do i need --twopassMode ?
Scholar 3 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Centurion 6 months ago, created 100 posts.
Good Answer 7 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 7 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 8 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Supporter 10 months ago, voted at least 25 times.
Appreciated 10 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Appreciated 11 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Teacher 16 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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