User: Macspider

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Macspider1.2k
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Posts by Macspider

<prev • 253 results • page 1 of 26 • next >
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Answer: A: Extracting string from every other line
... cat FILE.fasta | sed -e s'/.*gene:/>/'| sed -e s'/gene_biotype.*gene_symbol://' | sed -e s'/description.*//' | awk -F " " '{if (substr($0, 0, 1)==">") {print $1"|"$2} else {print $0}}' This will: 1. substitute everything which comes before "gene:" with just ">" 2. remove the part be ...
written 1 day ago by Macspider1.2k
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Comment: C: Adaptors Sequences and Trimming
... Are these homework questions? They look like! ...
written 1 day ago by Macspider1.2k
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Comment: C: Augustus gene prediction for non model organism
... I used bam2hints to calculate only introns, with `--intronsonly`. However, this flag is deprecated because it's the default now so shouldn't be the issue. How did you sort your bam file? By name or by coordinate? ...
written 7 days ago by Macspider1.2k
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Comment: C: GO Terms retrieval
... Could you perhaps close this one so that everyone goes to the other you opened? ...
written 14 days ago by Macspider1.2k
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Answer: A: Augustus gene prediction for non model organism
... I benchmarked gene prediction with Augustus for around 1 year. The standard procedure includes: 1. Mapping of RNASeq reads (bam output) 2. Obtain intron hints with **bam2hints** 3. Obtain coverage bigwig file with **bam2wig** 4. Obtain exon hints with **wig2hints** 5. Combine hints into gff h ...
written 14 days ago by Macspider1.2k
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How to retrieve Blast nr database dimensions?
... Hi guys, sorry if I look dumb (I do feel that way now). I am going through info pages, citations and database metrics of Blast since this morning because I need to find these infos: - Number of sequences in the non-redundant protein database (nr) - Number of sequences in the non-redundant nucl ...
nucleotide database sequence protein blast written 17 days ago by Macspider1.2k • updated 17 days ago by Sej Modha1.5k
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... Programs are made on test data. Actual data are different, and not always working in programs that should be made for every kind of data. I modify scripts all the time to adapt them to my needs! Hope this is not the case, but sometimes you just happen to spot a bug. ...
written 17 days ago by Macspider1.2k
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Comment: C: Help regarding RNA-seq STRINGTIE pipeline and output
... STRG should be the prefix for any newly assembled transcript apart from the ones in the provided `-G`. ...
written 27 days ago by Macspider1.2k
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... Are you sure this is the code block? This seems to me the code section where they check if quality and length are a positive number before doing analysis. It should be something like: if (single_qual_threshold >= qual_threshold) { > PROCEED < } else { > DISCARD < ...
written 27 days ago by Macspider1.2k
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... Could you paste the code block where these arguments are parsed? (if python argparse, perhaps paste also the head of the script where they are declared!) ...
written 28 days ago by Macspider1.2k

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Student 9 weeks ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 9 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 10 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 11 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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