From f9dc929f0470c520bc0f6e61349c41d25b87eab5 Mon Sep 17 00:00:00 2001 From: scythe Date: Fri, 22 Sep 2023 11:00:43 -0700 Subject: [PATCH 1/2] g-zipped versions of files not present. Corrected call accordingly --- docs/mapping.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/mapping.md b/docs/mapping.md index 08dfd2d..c5b1ad4 100644 --- a/docs/mapping.md +++ b/docs/mapping.md @@ -41,8 +41,8 @@ bowtie2-build pO157_Sakai.fasta.gz pO157_Sakai Now we are ready to map our reads ```bash -bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq.gz \ - -2 SRR957824_trimmed_R2.fastq.gz -S SRR957824.sam +bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq \ + -2 SRR957824_trimmed_R2.fastq -S SRR957824.sam ``` The output of the mapping will be in the SAM format. From 508b4215613a67974db48783d77513c69a77fb25 Mon Sep 17 00:00:00 2001 From: scythe Date: Fri, 22 Sep 2023 11:39:24 -0700 Subject: [PATCH 2/2] new invocation of mpileup as bcftools command ... instead of samtools --- docs/mapping.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/mapping.md b/docs/mapping.md index c5b1ad4..ca564b1 100644 --- a/docs/mapping.md +++ b/docs/mapping.md @@ -95,8 +95,7 @@ For an EHEC O157 outbreak you could use it to identify the source, for instance. We can call the variants using `samtools mpileup` ```bash -samtools mpileup -uD -f pO157_Sakai.fasta.gz SRR2584857.sorted.bam | \ - bcftools view - > variants.vcf +bcftools mpileup -f pO157_Sakai.fasta.gz SRR2584857.sorted.bam ``` You can read about the structure of vcf files [here](file_formats.md).