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ValueError: range() arg 3 must not be zero #1
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Hi @xiangyupan, thank you for your interest in IRescue. Could you check if the files Cheers |
Ok, this narrows down the problem. One reason could be that bedtools and/or samtools are not in your user's PATH. I noticed that you executed IRescue from |
Please, when you run irescue, add the options |
Hi bepoli, |
Hi @xiangyupan ,
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Hi, All.TE.deal.random100.bed.txt |
Hi @xiangyupan, No problem, thank you for getting back to me. I have found and fixed two tiny bugs that could cause your problem. I think that the read names in your BAM file end with So let's try this:
If you still receive the error, then there is something else that we need to check, but at least we would rule out a couple of possible bugs. |
Good! |
Hi @bepoli. Thanks for this great method. I'm using IRescue v1.0.2 and encountering this same problem.
Here's the IRescue output from my run.
And here are the heads from
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Hi @mikecuoco, thank you for the detailed report. Could you paste here a few lines from your BAM file? Let's also check the integrity of the header: could you run |
Hi @bepoli, thanks for the quick response! It turns out STARsolo does not include the CR and CB tags by default. I added the following line to my STARsolo call and IRescue works fine now.
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Great! I'm happy to hear that! |
Hi,
Thanks for the nice job in bioRxiv, hope it will be successfully accepted in a good journal.
Now I want to use it to quantificate my single-cell RNA-seq data.
An error occurred when I ran the command
nohup ~/anaconda3/envs/irescue/bin/irescue -b possorted_genome_bam.bam -p 8 -r /public1/home/sc60481/Axolotl/sc-RNA/03.deal.TE/All.TE.deal.bed -w ./filtered_feature_bc_matrix/barcodes.tsv.gz &
. I am not sure what caused the error.Hope for your reply and help.
Thanks for your time and work.
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