Hello everyone!

I am trying to perform mapping for ChIPseq samples with Bowtie2- and getting error every single time.

Explanation:

My samples were run in 2 different lanes and paired end sequencing was performed. Firstly I merged the reads (R1 and R2) from both lanes for each sample. Using below command

cat ShNTC.S1.L001.R1.fastq ShNTC.S1.L002.R1.fastq > ShNTC.S1.R1.fastq

cat ShNTC.S1.L001.R2.fastq ShNTC.S1.L002.R2.fastq > ShNTC.S1.R2.fastq

1) I tried trimming the adapters from both the reads and then running bowtie2, and got the following error.

Cuatadapt Command:

cutadapt -a file:Read1.fasta -A file:Read1.fasta -o ShNTC_S1_R1.fq -p ShNTC_S1_R2.fq ShNTC_S1_R1.fastq ShNTC_S1_R2.fastq

Bowtie2 Command:

./bowtie2 -q -x /data_local/public/hg19 -1 ShNTC_S1_R1.fq -2 ShNTC_S1_R2.fq -S

Error:

Error: 0 mate files/sequences were specified with -1, but 1 mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2. Error: Encountered internal Bowtie 2 exception (#1)

2) Just to try then I used the fastq files without trimming the adapters and I still encountered the same error.

Bowtie2 Command:

./bowtie2 -q -x /data_local/public/hg19 -1 ShNTC_S1_R1.fastq -2 ShNTC_S1_R2.fastq -S

Error:

Error: 0 mate files/sequences were specified with -1, but 1 mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2. Error: Encountered internal Bowtie 2 exception (#1)

I read somewhere that one could peroform fastq repair, why would that be needed and if and how would it help. Any pointers in this direction will really help me. Thank you very much.

Best, Priya