User: michael.ante

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michael.ante2.1k
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Posts by michael.ante

<prev • 228 results • page 1 of 23 • next >
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Comment: C: Looping local blastn in bash
... It should be something like: for file in *fasta do blastn -in $file -db dbGOI.fasta -out blast$(basename $file .fasta).txt done For explanation: the variable yyou use to loop is called file. You call this variable in with $file . to get the name of the fasta without the file-end ...
written 4 days ago by michael.ante2.1k
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Comment: C: GNU parallel on multiple files to re-header bam files
... Hi, if it works with the command lines, why not putting these into a bash script and running this bash script with parallel? Otherwise, you may use a tab-separated file where you have input and output variables stored like [here][1]. Cheers, Michael [1]: https://www.gnu.org/software/parallel/ ...
written 6 days ago by michael.ante2.1k
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Answer: A: How to get human miRNA length file?
... Hi, Where did you get the counts from. If it was a gtf/gff or bed file, you can use it to extract the length. Otherwise, you can use for instance [biomart][1] or [RFAM][2] to get the information you need. Nevertheless, you should think of using a different normalisation method, since miRNAs' lengt ...
written 6 days ago by michael.ante2.1k
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Answer: A: To obtain excel expression file
... Hi, Please have a look at this paper [Zeeberg et al. **2004**][1]. Not only automatical name interpretation, but also float to time conversions are usually made by Excel. An RPKM of 28.09 may be converted as the date 28th of September. As an apprentice in Bioinformatics, you may want to learn R or ...
written 10 days ago by michael.ante2.1k
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Answer: A: two genes within same genomic region
... Hi Mike, These two genes are on different strands of the chromosome. This is quite usual and nothing to worry about. Cheers, Michael ...
written 10 days ago by michael.ante2.1k
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Comment: C: fastqc adapter content
... The overrepresentation in FastQC is computed on the reads' first 50 bp. Your adapter sequences are popping up further downstream. ...
written 12 days ago by michael.ante2.1k
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Answer: A: How to present mapping result ?
... Most aligners have a decent mapping summary log. You could rely on these, or you can try RSeQC's bam_stat.py. I'm usually not using samtools flagstat, since it is summarising rather alignments not reads. For comparing different samples, you can use multiQC. ...
written 17 days ago by michael.ante2.1k
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Answer: A: Extract random number of transcript and exons from gencode annotation
... Hi Zoegward, I think you need to extract 1000 transcript IDs from the gtf. Something like awk '$3=="transcript" && match ($0, /protein_coding/){for(i=1;i transcript-list.txt To extract all Transcript IDs from protein coding genes. In order to get 1000 IDs just uses `head -n 1000`, `t ...
written 18 days ago by michael.ante2.1k
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Comment: C: Sequence Length Distribution From A Fastq File
... Between print and length should be at least one space. If you want to compute the number of reads simultaneously, use something like [Frèdèric's approach ][1] awk 'NR%4 == 2 {lengths[length($0)]++ ; counter++} END {for (l in lengths) {print l, lengths[l]}; print "total reads: " counter}' file.f ...
written 21 days ago by michael.ante2.1k
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Comment: C: rna-seq analysis of tumor/normal pairs
... DESeq2 has a method implemented called independent filtering, which is called in the standard setting. Other than that, you can use R functions like `which` and `rowSums` to filter your gene count table. I would refrain from that since you remove information used for applying dispersion estimation. ...
written 4 weeks ago by michael.ante2.1k

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