User: Macspider

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Macspider3.0k
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Posts by Macspider

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Comment: C: Extract allele read counts for heterozygous positions in VCF
... Yes, I am afraid so. If this information is not stored during the pileup, it won't be possible to extract it from a VCF file. ...
written 5 weeks ago by Macspider3.0k
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Answer: A: Extract allele read counts for heterozygous positions in VCF
... When you do the pileup, for example with samtools, you can require additional tags to be present in your `INFO` and `GENOTYPE`. These are specified via the `-t` option. I usually ask for: −t DP,AD,ADF,ADR,DP4 Note that DP4 is deprecated but still present in the output if you require it. It con ...
written 5 weeks ago by Macspider3.0k
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Comment: C: Trimmomatic; How to get only q20 < q < q30 reads
... Have as much as you need within programs that you can re-run at any time, save all logs possible. This is really 90% of the efficiency, imho! Everytime something like this happens, you be like changing your script parameters and re-run it. Even if it took a lot to get where you are, re-running it wo ...
written 5 weeks ago by Macspider3.0k
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Comment: C: Trimmomatic; How to get only q20 < q < q30 reads
... I work routinely with FASTQ files that are > 500GB and I would repeat the whole analysis ^^ putting every command into a script doesn't take so long, after all, if they execute one after the other. ...
written 5 weeks ago by Macspider3.0k
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Comment: C: cutoff for expressed genes in DESeq2
... This might be the best suggestion you'll ever receive about it. ...
written 5 weeks ago by Macspider3.0k
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Answer: A: cutoff for expressed genes in DESeq2
... This is a very "philosophical" question, but to cut it short, many people in the past have used a minimum threshold of FPKM >= 1. This value is extremely eye-metric and not based on robust statistics. It will, however, eliminate a lot of noise, and it will be easy to reference why you chose tha ...
written 5 weeks ago by Macspider3.0k
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Comment: C: Remove part of headers in FASTA file
... On the same train of thought as @genomax, I would say that also brackets, pipes and equals could be avoided. Not because they could damage you *now*, but because you'll never know what you'll need these data for in the future. Those characters could easily mess up your future pipelines! Something ...
written 5 weeks ago by Macspider3.0k
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Comment: C: Remove part of headers in FASTA file
... I edited the command in my first comment. It now has a start `*` after the numeric specification `[0-9]`. This means that any *sequence of numbers* from 0-9 will now be deleted. ...
written 5 weeks ago by Macspider3.0k
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Answer: A: Remove part of headers in FASTA file
... cat $filename | sed 's/>.*cds_/>/' | sed -e 's/_[0-9]* \[/ \[/' *First sed* Each character (.*) that is contained between `>` and `cds_` is replaced by only `>`. This leaves the FASTA header intact but removes everything until `NP_`. *Second sed* Enabling regular expressions (` ...
written 5 weeks ago by Macspider3.0k
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Answer: A: TPM or FPKM for single cell RNA seq experiment ?
... The community is generally more used to FPKM but the author of FPKM itself said that we should move on because it is biased ([ref][1]). Also, you can convert FPKM to TPM using [a formula][2]. And if you can't access that formula, I also report it in [one of my papers][3] (see methods section "ΔXT/F ...
written 5 weeks ago by Macspider3.0k

Latest awards to Macspider

Scholar 5 weeks ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 3 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 3 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Scholar 3 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 5 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Great Question 8 months ago, created a question with more than 5,000 views. For Remove duplicates from reads: best practices?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Popular Question 11 months ago, created a question with more than 1,000 views. For DESeq2 proper design setting
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 11 months ago, created a post with more than 5 votes. For A: Explanation of a Perl script
Great Question 11 months ago, created a question with more than 5,000 views. For Best way to compare two samples in a VCF file
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Scholar 13 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 16 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Good Question 16 months ago, asked a question that was upvoted at least 5 times. For Best way to compare two samples in a VCF file
Popular Question 17 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 20 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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