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Have I written this correctly?
Hi, I'm in a group investigating gene editing in wheat using CRISPR/Cas9 and we have the Illumina MiSeq sequencing results but I am unsure how to succinctly present the analysis we did (I have next to no understanding of bioinformatics- I did not do the analysis myself but am writing it up for an undergraduate report).
I was therefore wondering if the following made sense (I have all the individual commands which I will put in the supplementary materials). This is my best shot so far (I've had to anonymise names until results are published):
Initial sequence quality was checked using FastQCv0.10.1. Illumina adaptor sequences were then removed using cutadapt version 1.14. Reads were then trimmed by quality score using fastq-mcf (Version: 1.05.676). A custom perl script was then run on reads to separate samples used in this study from ----- ------’ (University of ****, UK) samples. To ensure the bowtie2 aligner could be used, pairfq (version 0.17.0) was used to create new fastq files that only contained mate pair reads. Bowtie2 index for reference sequences was then built. Sequence alignments for each set of reads was then set up and sam tools were used to convert sam (Sequence Alignment Map) alignment files to a binary bamfile, this was then sorted and a bam index was created. Bam files were visualised using the Tablet software. Refer to supplementary information for individual commands.
Does this make sense? What else (and where in that paragraph) should I have included?
Any help would be extremely well appreciated.
Thank you so much
I was therefore wondering if the following made sense (I have all the individual commands which I will put in the supplementary materials). This is my best shot so far (I've had to anonymise names until results are published):
Initial sequence quality was checked using FastQCv0.10.1. Illumina adaptor sequences were then removed using cutadapt version 1.14. Reads were then trimmed by quality score using fastq-mcf (Version: 1.05.676). A custom perl script was then run on reads to separate samples used in this study from ----- ------’ (University of ****, UK) samples. To ensure the bowtie2 aligner could be used, pairfq (version 0.17.0) was used to create new fastq files that only contained mate pair reads. Bowtie2 index for reference sequences was then built. Sequence alignments for each set of reads was then set up and sam tools were used to convert sam (Sequence Alignment Map) alignment files to a binary bamfile, this was then sorted and a bam index was created. Bam files were visualised using the Tablet software. Refer to supplementary information for individual commands.
Does this make sense? What else (and where in that paragraph) should I have included?
Any help would be extremely well appreciated.
Thank you so much
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