multiple sequence files

[shlomobl]

Dear all, I got 4 fastq files from seq provider (L1 to L4) instead of 2 as I was used to get with another provider. They told me is it because sequencing was done with Nextseq. The question is how to accommodate 4 files in the metadata file for tormes? Best, Shlomo

[nmquijada]

Dear @shlomobl Are those fastq files from different samples? Were they performed by paired-end sequencing (regardless the Illumina platform)?

[shlomobl]

Yes, same organism, paired-end. I actually got a new set of files for these samples (they were re-sequenced) but it would be nice to know how to deal with that for future reference. Best, Shlomo

[nmquijada]

Hi Shlomo, If I understood well, you have several forward (R1) and reverse (R2) reads fastq files for the same organism. In such situations, you can merge all the forward and reverse reads that you have for the same organism in two different files, for forward and reverse reads, respectively. You can do it as follows:

cat file-1_R1.fastq.gz file-2_R1.fastq.gz file-N_R1.fastq.gz > all_R1.fastq.gz
cat file-1_R2.fastq.gz file-2_R2.fastq.gz file-N_R2.fastq.gz > all_R2.fastq.gz

Then, use those all_R1.fastq.gz and all_R2.fastq.gz for the metadata file. Let me know if it worked! Narciso

[Narges-sys]

Hi Narciso, I have a question for you. Is it possible to put R1 and R2 reads of several samples in one metadata file?

Best of all, Narges

[nmquijada]

Hi Narges,

Sure! That is the purpose of the metadata file: that you can have as many samples as you want by specifying the locations to the R1 and R2 files, in only one metadata file. Maybe you can take a look to this section of the wiki: https://github.com/nmquijada/tormes/wiki/Shortcut-to-generate-the-metadata-file-for-TORMES

Did it solve your question? Best, Narciso

[ariasamin]

Dear Narciso, Thank you for your reply. Absolutely. It was a great help. All the best, Narges

[nmquijada]

Dear Narges,

Happy to read that! Do not hesitate to reach out if you have further queries ;)

Best, Narciso