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Hello everyone,
I am relatively new to NGS data analysis , however I have managed to learn how to analyse RNA-seq and CHIP-seq data. I have written some basic python scripts to automate the steps and they had been working up until recently, meaning I have gotten results such as txt files from differential expression analysis after quantification or valid files from peak calling. I stopped using my scripts for about 2 weeks since i didnt have any more data for that period and when i came back 3 days ago and tried to analyse several new sets of sra files from GEO , the same error keeps occuring for every file that i am trying to analyse. Basically the error occurs right after the alignment with bowtie2 when i try to convert the sam files to bam showing a parse error at a specific line or incomplete aux field. Any help would be greatly appreciated. I also apologise if this format is not the proper one for questions, it is my first time asking for help in forums in general. I am mentioning the commands because the error occurs both when i run my script and when i just write the commands manually in the terminal for each file.
commands : bowtie2 -p 6 -x {genome_index_path} -U {fastq-file} -S {output-sam-file}
samtools -b -o {output-bam-file} {output-sam-file}
I am relatively new to NGS data analysis , however I have managed to learn how to analyse RNA-seq and CHIP-seq data. I have written some basic python scripts to automate the steps and they had been working up until recently, meaning I have gotten results such as txt files from differential expression analysis after quantification or valid files from peak calling. I stopped using my scripts for about 2 weeks since i didnt have any more data for that period and when i came back 3 days ago and tried to analyse several new sets of sra files from GEO , the same error keeps occuring for every file that i am trying to analyse. Basically the error occurs right after the alignment with bowtie2 when i try to convert the sam files to bam showing a parse error at a specific line or incomplete aux field. Any help would be greatly appreciated. I also apologise if this format is not the proper one for questions, it is my first time asking for help in forums in general. I am mentioning the commands because the error occurs both when i run my script and when i just write the commands manually in the terminal for each file.
commands : bowtie2 -p 6 -x {genome_index_path} -U {fastq-file} -S {output-sam-file}
samtools -b -o {output-bam-file} {output-sam-file}