Open Mondlii opened 2 years ago
Hello, please paste the command you run to get the mapped.sam file.
Best regards, Robert
Hi, thank you for your response.
The command I used:
bwa mem -t 8 bridge_contigs/bridged_contigs.fasta /Macrogen_datqa/ILPE_unclassified_1.fastq /Macrogen_datqa/ILPE_unclassified_2.fastq> /nlustre/users/Macrogen_datqa/map_nanopore.sam
Please run head -n1 ILPE_unclassified_1.fastq
and the same for ILPE_unclassified_2.fastq
.
ILPE_unclassified_1.fastq "@A00721:395:H7GYTDSX3:4:1101:1181:1000 1:N:0:CGGAACTG+TCGTAGTG" ILPE_unclassified_2.fastq
"@A00721:395:H7GYTDSX3:4:1101:1181:1000 2:N:0:CGGAACTG+TCGTAGTG"
Please rerun bwa-mem with the combined file ILPE_joined.fastq. The problem is that reads after the preprocessing script have different names in .fastq and in your .sam file, and Racon will disregards all overlaps.
Hi Racon,
I am trying to use Racon to polish an assembly using my illumina data. I've been able to polish using just the long reads, but I am having issues doing the same with illumina data. I have looked at all previous versions of this issue and I am still having a hard time trying to solve the issue. I saw the latest post suggested using the latest version, but the latest version I can get through conda is 1.4.20 and the school is very strict and limiting with building and installing outside of conda environments.
I have used a previously mentioned script to merge my pe reads into one file, and that didn't give any errors,