Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Third FASTQ containing UMI sequences #1205

Open
wants to merge 4 commits into
base: fastquorum
Choose a base branch
from
Open

Third FASTQ containing UMI sequences #1205

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
fbc073f
Add 3rd FASTQ file containing UMI sequences for the duplex-seq tiny d…
adamrtalbot May 15, 2024
9452520
README
adamrtalbot May 15, 2024
5c327ef
Use branch path until merge is ready
adamrtalbot May 15, 2024
4b30e0f
Split sample IDs in test data because they can't have different read …
adamrtalbot May 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,10 +66,16 @@ seqtk sample -s 42 SRR6109255_1.fastq.gz 0.01 | gzip -c > tiny/SRR6109255_1.fast
seqtk sample -s 42 SRR6109255_2.fastq.gz 0.01 | gzip -c > tiny/SRR6109255_2.fastq.gz
```

A FASTQ of only the UMI sequences was generated by slicing the first 10bp from the sequencing data in the R1 FASTQ file using fastx:

| tool | version |
|---------|----------|
| `seqtk` | 1.4-r122 |
```console
gunzip -dc testdata/duplex-seq/tiny/SRR6109255_1.fastq.gz | fastx_trimmer -f 1 -l 10 -z -o testdata/duplex-seq/tiny/SRR6109255_3.fastq.gz
```

| tool | version |
|---------------|----------|
| fastx_toolkit | 0.0.14 |
| `seqtk` | 1.4-r122 |

### Reference Information

Expand Down
Binary file added testdata/duplex-seq/tiny/SRR6109255_3.fastq.gz
View file
Open in desktop
Binary file not shown.
5 changes: 3 additions & 2 deletions testdata/duplex-seq/tiny/samplesheet.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
sample,id,single_end,fastq_1,fastq_2,read_structure
SRR6109255,SRR6109255,false,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_2.fastq.gz,10M1S+T 10M1S+T
sample,id,single_end,fastq_1,fastq_2,fastq_3,read_structure
SRR6109255,SRR6109255,false,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_2.fastq.gz,,10M1S+T 10M1S+T
SRR6109255_2,SRR6109255_2,false,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/duplex-seq/tiny/SRR6109255_2.fastq.gz,https://github.com/nf-core/test-datasets/raw/fastquorum_umi_fastq_file/testdata/duplex-seq/tiny/SRR6109255_3.fastq.gz,11S+T 11S+T +M