migec
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mikessh
A RepSeq processing swiss-knife
Hi, mikessh, what's the differences of overseq-units.txt compared with overseq.txt, pwm-units.txt compared with pwm.txt ? how to calculate them?
Hi, I have an old MIGEC v1.2.9 package. It could not work under the new version of Java 17 in Linux CentOS 7. How to make it work. Thanks. Best...
I try to understand what the --overlap-max-offset X setting control. We do Pair end reads 150+150, and our amplicons are roughly 200bp, so I assume that our read-through is high....
Hello, I am running migec-1.2.9 on canine paired TCR seq data for UMI extraction. I tested one sample (R1 & R2) by running Checkout manual, since I am planning on...
Something is getting corrupted when Checkout is compressing its output. This is causing Histogram to give an `invalid block type` error. I've pasted the trace from Histogram below, but the...
Dear mikessh, I must apologize to you in advance if my question is very tedious or make no sense to you. I'm very new to repertoire analysis and do not...
Following the documentation, I usually choose a single, "reasonable" oversequencing threshold from those reported by MIGEC in the histogram step of the various sample: > In most cases, the automatic...
Hello mikessh, Migec incorrectly identified reads by matching sequences mid-read to the barcode provided while ignoring the correct barcode at the beginning of the read (no mismatches, etc.). Barcode file:...
Hi Mikhail, I would like to deduplicate Qiagen Tcr libraries using the UMI present in the Qiagen Immune repertoire workflow. I saw in your Readme (https://migec.readthedocs.io/en/latest/index.html) that TRA is not...
Hello, I am trying to use MIGEC to demultiplex some single cell sequencing data generated using a MiSeq. To do this I have made a whitelist of cell barcodes possibly...
