Elton Vasconcelos

spades-hammer finished abnormally, OS return value: -7

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### Description of bug Dear Spades Team, I'm getting this spades-hammer error after 38 hours of metaspades assembly process. ####### == Error == system call for: "['/nobackup/fbsev/bioinformatics-tools/SPAdes-3.15.4-Linux/bin/spades-hammer', '/nobackup/fbsev/LeedsOmics/DougStewart-Jan22/metaWRAP-run/ASSEMBLY_A/metaspades/corrected/configs/config.info']" finished abnormally,...

Dear Jaswinder, Congrats for the great work! I wonder if there is an option to switch off the drawing of both blue and green lines (representing pseudo-knots and/or non-canonical base...

readLength option from importIsoformExpression for stringtie on ONT long read sequencing

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Dear Kristoffer, Thanks for developing and maintaining this tool. I just want to ask a quick question on what to set as "readLength" on the importIsoformExpression function for Stringtie outputs...

duplicate patients removed when I set params.txt not to do this

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Dear MutSig2CV team, Even setting params.txt not to remove duplicate patients, my execution is doing that anyways. -------------------- MUTSIG_VERSION = 2CV v3.11 LOADING DATA Processing target list. Loading mutations... Keeping...

m6anet dataprep error

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Dear developers, I've already successfully run the full m6anet pipeline (version 2.0.1) on a given dRNA-Seq dataset, but now am experiencing the following error during the dataprep step on a...

Detection of 5mC without TET

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Hello, I am currently with 92x genome coverage (with pacbio reads) and successfully predicted the 6mA and 4mC positions on the genome (running ipdSummary with the "--identify m6A,m4C" flag). I...

KeyError: 'IPD'

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Hello folks, I believe I am almost there attempting to run ipdSummary smoothly. Could you please check the attached log file out and give me some support to solve that....

Hello pacbio bifx folks, Can anyone help me with the following log. I appreciate your attention in advance! *_$ nice ipdSummary.py --reference genome.fa --outfile baxh5-vs-ref.ipdSummary --numWorkers 20 -v baxh5-vs-Sm_v5p2.cmp.h5 >...

System.MissingMethodException: Method 'Array.Empty' not found

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**Describe the bug** Trying to run Rawtools for quality control analysis along with a database search on TMT10 raw data which has an empty channel. **Description of raw file** MS2...

differential m6A methylation between sample groups

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Dear m6A developers. I wonder if you can advise on the best statistics to perform a differential m6A abundance analysis between two sample groups. I've already successfully run m6anet v2.1...