Thank you so much!... At first, I don't clearly understand the different lane and read because there are only 2 fastq files in the public data... As suggested, I merged the two files from the same read using concatenate, I did the bowtie2 for the two reads and I get 99.24% alignment...
Do you have any opinion about the use of Merge Tool like Flash & Pandaseq to merge the data? There are some comments that there will be some data loss if you just concatenate to merge the data...
But seeing the good % of alignment, I think "concatenate" works well
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maisarasora •
If you want people to help, show your command lines.
bowtie2 -p 8 -N 1 --no-mixed mode --no-discordant -x $REF -1 IN1_S1_L001_R1_001.fastq -2 IN1_S17_L002_R1_001.fastq -S /mnt/e/sequence_data/ChIP-seq/FASTQ/14INPUT/bams/IN1R1.sam
this is the command line that I used
IN1_S1_L001_R1_001.fastq, L001 and L002 means different lanes, R1 and R2 means read1 and matched read2. so you should use R1F=IN1_S1_L001_R1_001.fastq, R1R=IN1_S1_L001_R2_001.fastq as input 1 and 2, or merge the different lane data into a one data, then use bowtie2.
Thank you... I also tried that approach.. At first I don't clearly understand about the different lane and read because there are only 2 fastq files in the public data... As suggested below, I'm now merging the two files from the same read using concatenate, I did the bowtie2 for the two reads and I get 99.24% alignment...
Do you have any opinion about the use of Merge Tool like Flash & Pandaseq to merge the data?
sorry, I just use cat command to add the fastq data, or use samtools merge to merge bam data
In public data there are only 2 files (R1 and R2) because the concatenation (the cat command) of the different lanes has already been performed. Recap:
To merge the different lanes, use
catTo merge different bam files (for example several replicates) use
samtools mergebowtie2 -p 8 -N 1 --no-mixed mode --no-discordant -x $REF -1 IN1_S1_L001_R1_001.fastq -2 IN1_S17_L002_R1_001.fastq -S /mnt/e/sequence_data/ChIP-seq/FASTQ/14INPUT/bams/IN1R1.samthis is the command line that I used
Why are you giving it two read 1 files as if they were matched pairs? That's never going to work.
I just realize that... I don't clearly understand the different lane and read because there are only 2 fastq files in the public data... I'm using concatenate to merge the data from the same read