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Answer: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
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> my guess is this would be cheaper/faster than just aligning all of them to the genome to begin with
If you are paying for all of your co…
Comment: Annotation Issue using miRBASE gff
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anthony.santana.703.j
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Thank you but, didnt make a difference, let me see what I can find, there has to be a reason.
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Thank you. Sorry, I should have prefaced that I was able to find canonical markers of these cells in my main cluster, which is a mixture of…
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>Troubleshooting Steps: Ran minimap2 manually on Pritchett’s reference (attraktion.fasta) and query (pt2_busco.fa); it generated a 442 MB .…
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That was an excellent idea. I used blastn to pull out all ONT reads containing some/all of the gene of interest and mapped that to the refe…
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Looking at the alignment file we know the reference chromosome names match the GTF from miRBase. So that should be fine. Your reads are als…
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samtools view:
LH00150:566:22TM3VLT3:6:2196:18797:12321_CTTTTCTGCCTA 16 chr1 10571 255 16M * 0 0 …
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"Wow those M-chips really are fast!" possibly this. Especially with the M4 (essentially a laptop chip) when it comes to single thread perfo…
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If the run stops at the same point in the pritchett file then you should examine that to see if there is any data corruption. Make sure the…
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There was nothing on SLURM logs, the error mentioned above is in the error file. For Madsen, log file looks similar but is complete. For Pr…
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I truly appreciate your clear and comprehensive explanation. I learned a lot of important and practical points.
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If you were planning to do comparisons, should you not make sure that the software versions were identical on both platforms. OpenJDK as w…
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Thank you for your comment. Now, I will go for interpretation
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That's open-ended. S…
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The code for scaling is `t(scale(t(x)))`, don't use apply here, that is inefficent. Before command is vectorized. If you use DEGs then by d…
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