User: michael.ante

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michael.ante2.7k
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Posts by michael.ante

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Answer: A: How to generate custom fasta and gtf files for RNA spike-ins
... Assuming the tRNAs are unspliced sequences, you can add them like the ERCC92 spike in annotation: Each spike in has its own contig and each gene annotation goes from start to the end. Something like: >mySpikeIn1 ACGA.... and the GTF: mySpikeIn1 spikein exon 1 9999 0.0 + . g ...
written 2 days ago by michael.ante2.7k
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Comment: C: Antisense transcription from strand specific RNA-seq
... Hi, According to the Hisat manual, the option just add the XS-tag to each alignment. To check the sence/antisense mappings, you might want to look at [RSeQC][1] infer experiment. There the read-orientation is analysed in regard of the transcripts' orientation. [1]: http://rseqc.sourceforge.ne ...
written 7 days ago by michael.ante2.7k
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Comment: C: how to extract counts from bam/merge-bam without gtf
... With samtools idxstat, you get a table of the contig name, the contig's length, the number of alignments, and the number of unmapped reads. Having such a table in R. you only need to select the first column as row names and the third column as the counts. You also might discard the last row. ...
written 7 days ago by michael.ante2.7k
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Comment: C: chimeric transcripts detection tool
... I know, that there's [STAR-Fusion][1]. But I don't know how it compares to the other mentioned tools. Cheer, Michael [1]: https://github.com/STAR-Fusion/STAR-Fusion/wiki ...
written 7 days ago by michael.ante2.7k
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Answer: A: how to extract counts from bam/merge-bam without gtf
... Hi Shahzad, If you have only the transcriptome annotation, I'd go for [Salmon][1] . In case your species has multiple transcript per gene, you might run into troubles with the multimapping reads. Per default bowtie2 reports one alignment per read(-pair). Even if you have several with the same scor ...
written 7 days ago by michael.ante2.7k
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Comment: C: % of reads unmapped: too short - STAR 2.5.2b
... Hi Clement, I'd try two things: 1st, align the 2 read sets separately and check if it works in principle. 2nd If that works, you can (visually) inspect if the R1 & R2 read overlap. If he overlap is quit big, you might need to go for the STAR 2.6 version with the --peOverlapNbasesMin parameter ...
written 8 days ago by michael.ante2.7k
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Comment: C: cause of unmapped short with STAR
... Please see this comment [here][1]. [1]: https://www.biostars.org/p/344286/#344329 ...
written 14 days ago by michael.ante2.7k
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Comment: C: The same qvalues are reported to different pvalues
... You may try to use the standard `p.adjust` with `method = "BH`" (which is the FDR-correction) on the hyper's pvalue. It may be that the parallel computing messed up the qvalues. ...
written 23 days ago by michael.ante2.7k
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Comment: C: Can one use STAR (splice-aware) to align genomic DNA (non-spliced)
... I'd check if you have spliced reads or not. In my experience, STAR aligns the reads correctly; even over exon-intron boundaries. But I'd be rather on the safe side. ...
written 26 days ago by michael.ante2.7k
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Comment: C: Faster way to get sequences from large fasta files?
... Wouldn't STAR-Fusion or Tophat-Fusion give you the insight you need? With these tools, you'll detect chimeric reads and search for those with one read in the nucleus and the other in mt. ...
written 26 days ago by michael.ante2.7k

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