Moderator: ATpoint

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ATpoint42k
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41,550
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Germany
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2 hours ago
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4 years, 7 months ago
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Posts by ATpoint

<prev • 6,110 results • page 2 of 611 • next >
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Comment: C: Very large fastq files from RNA-seq
... WIthout details on the pipeline this is impossible to answer. Please add comments via `ADD COMMENT/REPLY` to keep things organized. ...
written 2 days ago by ATpoint42k
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Comment: C: Differential Expression Analysis
... So essentially you have data and no idea what to do with them in terms of a biological question? What are you working on? There must be a reason you even started whatever you are doing. ...
written 3 days ago by ATpoint42k
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Comment: C: Mapping sequencing reads to 5-UTR, 3-UTR and CDS (fasta or gtf?)
... Fasta files have no positional information so yes, you cannot use it. GTF files have the information you want encoded, available from Ensembl, NCBI or GENCODE. From there you could use `coverage`. ...
written 3 days ago by ATpoint42k
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Comment: C: samtools index cannot index concatenated bam?
... As explanation, `cat` simply concatenates two files. Inappropriate for BAM files since they have header structures etc. `samtools cat` would be more appropriate whereas `merge` keeps the sort order. The `index` command requires coordinate-sorted files. In any case you have to sort the files, either ...
written 3 days ago by ATpoint42k
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Comment: C: Sort Sam file by chromosome and position in python
... https://pysam.readthedocs.io/en/latest/api.html ...
written 4 days ago by ATpoint42k
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Comment: C: Does the host of human coronaviruses (CoVs) genomes/sequences must be from human
... Don't waste your time with SE Biology, imho it is mostly a dumpster fire, quality of questions there is abysmal and I have the feeling therefore experienced users often do not even visit it to give good answers, so better post it in a suitable subReddit. This is no offense again SE in particular, ju ...
written 4 days ago by ATpoint42k
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Comment: C: Sort Sam file by chromosome and position in python
... Check `pysam` rather than coming up with costom solutions, it is the swiss-army knife for sequencing data manipulation in python. ...
written 4 days ago by ATpoint42k
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Comment: C: what is the meaning of "consensus mutation"?
... You received answers in many of your previous questions. Please take the time to upvote and accept helpful ones. ...
written 4 days ago by ATpoint42k
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Comment: C: Is there a reason for less IgG occupancy around the promoters of highly expresse
... It is difficult to comment on anecdotal descriptions without seeing plots and having details on how you processed data. ...
written 4 days ago by ATpoint42k
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Comment: C: error in sed usage
... That's not what I mean. Please give a representative example of the content of each variable so we know what it contains, not code, just a string what they contain. ...
written 5 days ago by ATpoint42k

Latest awards to ATpoint

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 4 days ago, created an answer that has been accepted. For A: Get sequence by genomic coordinates in R
Appreciated 5 days ago, created a post with more than 5 votes. For A: Get sequence by genomic coordinates in R
Scholar 5 days ago, created an answer that has been accepted. For A: Get sequence by genomic coordinates in R
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Popular Question 8 days ago, created a question with more than 1,000 views. For [[ Please read before posting a question ::: How To Ask A Good Question ]]
Scholar 9 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Prophet 10 days ago, created a post with more than 20 followers. For [[ Please read before posting a question ::: How To Ask A Good Question ]]
Scholar 11 days ago, created an answer that has been accepted. For A: Get sequence by genomic coordinates in R
Scholar 14 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 16 days ago, created an answer that has been accepted. For A: Get sequence by genomic coordinates in R
Scholar 17 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 18 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 18 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Appreciated 21 days ago, created a post with more than 5 votes. For A: Get sequence by genomic coordinates in R
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 26 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Good Answer 26 days ago, created an answer that was upvoted at least 5 times. For A: Get sequence by genomic coordinates in R
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Teacher 26 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?

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