sample split in multiple flowcells and lanes

Hi All!

I am analyzing scRNAseq data. Unfortunately, I have the same sample split in multiple flowcells (2) and multiple lanes (2). I have read that there is no problem merging the fastqs files from different lanes. I am wondering if I can then merge the merged fastq (by lanes) by flowcells.

Thank you!

scrnaseq

• 861 views • link

updated 4.4 years ago by swbarnes2

• written 4.4 years ago by pingu77 •

1 answer

If it's the exact same library, cat it together, no matter how many lanes or flowcells it is distributed on.

• 0 views • link

written 4.4 years ago by swbarnes2

More posts like this

RNA-Seq multiple lane
written 1.9 years ago by MaxMin •

Hello everyone, I have paired-end fastq files from different lanes. When is it most appropriate to merge them during a transcriptomic analysis? The files are …
Fastqs different lanes
written 3.3 years ago by samuel

Can anyone please confirm the following. - You should generate sam/bams with read groups for downstream analysis (GATK) - If you have fastqs from the …
Same sequencing sample in multiple lanes. How to analyse it?
written 4.4 years ago by Federico •

Hi, I have the following samples: **Lane 1**: - 184631_S1_L001_trimmed_R1.fastq - 184631_S1_L001_trimmed_R2.fastq **Lane 2**: - 184631_S1_L001_trimmed_R1.fastq - 184631_S1_L001_trimmed_R2.fastq I would like to align these fastq …
Merging FASTQs from the same sample
written 4.6 years ago by adellegreene •

Hello, I have a question regarding merging FASTQ files from the same sample but different sequencing runs. We generated cDNA libraries using the 10X v3 …
snakemake to merge bams from multiple samples
written 5.1 years ago by samuel

Hi, I have multiple sample bams which are split over two lanes. e.g. for 2 samples: flowcells: ["CCGB1ANXX-", "CCHNTANXX-"] samples: ["3666-02-45-1_S2", "3666-03-45-1_S3"] lanes: ["L005", "L006"] …
How I deal with different lanes in RNA-seq alignment
written 6.9 years ago by zizigolu

Hi I have Four lanes per sequencing run => 4 fastqs each so for each patient I have 16 Fastq files I am using STAR …
Trimmomatic: Does it matter to trim the fastq before or after merging multiple replicates?
written 10.0 years ago by tunl

For each sample, we have a group of replicates fastq files (which came from different lanes). To do analysis, we merge the multiple replicates fastq …
tophat-fusion for gene fusion detection
written 11.2 years ago by Jackie

I am trying to use tophat-fusion for gene fusion detection. My data (fastq files) are paired-end, and I have fastq files from multiple lanes, and …
Using an aligner with parallel threading (bowtie2) how much faster is aligning then merging vs. mer…
written 11.3 years ago by kaston •

I have a sample that has multiple fastq files, one for each lane that it was sequenced on. I was planning on merging these fastqs …
Fastq Files From Different Flowcells
written 13.0 years ago by hellbio

<p>Hi,</p> <p>For a single sample, i have several paired-end fastq files from four different flowcells. i.e. fastq files from different lanes from each flowcell. Instead …