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That is probably fine since you are counting only the miRNA using that GTF. You already compressed the data by desuplicating UMI. Take a lo…
Comment: Annotation Issue using miRBASE gff
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Hello Geno,
I figured out part of my issue, my gtf file was corrupt, and I also changed my featureCounts params:
featureCounts -F GTF…
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Honestly, I'd just stick with `STAR` for this purpose. You can use the `--outReadsUnmapped` option to directly output the unmapped reads in…
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Did you remove invariant (constant) sites from the SNP alignment? If so, you should probably also be specifying an ascertainment bias corre…
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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…
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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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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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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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