Excluding all info other than SRR ID

[GitTodojetaime]

I am on lesson 1 exercise and struggling to exclude all information in my output that is not the SRR ID. Here are my commands:

touch read.names.txt (creating the file for NA12878.fastq sequence data)
seqkit seq --only-id NA12878.fastq | head (extracting the sequence SRR ID only)

I am very new to this. Thank you for any suggestions!

[robertaboukhalil]

Hello! A few pointers:

• What does seqkit seq --only-id NA12878.fastq | head output? Does it output only the SRR IDs, or also the rest of the FASTQ entry?
• Refer to https://sandbox.bio/tutorials/seqkit-intro/3 for info on how to extract just the IDs and not the rest of the FASTQ entry

Hope this helps!

[GitTodojetaime]

It outputs all of the rest of the FASTQ entry.

[GitTodojetaime]

So I tried this.. seqkit seq --name --only-id hairpins.fa | head..after opening the file the sequencing read names were saved in. I generated an output of ID's only that looks correct but my tutorial isn't marking it as correct. Let me know what you think.

[robertaboukhalil]

Ah, looks like you're using the wrong file! It should be NA12878.fastq, not hairpins.fa, so seqkit seq --only-id --name NA12878.fastq > read_names.txt