See [Submitting NGS sequences to NCBI SRA](https://sarahtanja.github.io/quarto-blog/posts/ncbi-sra-submission/ncbi-sra-submission.html) lab notebook post on instructions

each sample has 4 files to upload:

-   R1 fastq.gz

-   R1 fastq.gz.md5

-   R2 fastq.gz

-   R2 fastq.gz.md5

submission upload says it is missing files for samples `7C14` and `89C14`

```{r, engine='bash'}

ls ../data/*7C14*
```

```{r, engine='bash'}

ls ../data/*89C14*
```

The files are in our data folder so they must have not made the upload on the NCBI end

How many total files need to transfer?

```{r, engine='bash'}

ls -1 ../data/*fastq* | wc -l
```

252 files transferred! 4 files for each sample, and we have 63 samples.

::: callout-warning

**Warning:**

:   456L9_S42_R2_001.fastq.gz.md5 may be corrupted. If it is an archive, please re-compress it and upload it again.\
    Please double check that you had uploaded the correct file(s)
:::

```{r, engine='bash'}
cd ../data/
md5sum -c 456L9_S42_R2_001.fastq.gz.md5 #check if the md5sum is OK
md5sum 456L9_S42_R2_001.fastq.gz.md5 #write out checksum 
```

The checksum looks good, I just clicked 'submit' again and it went through.

Status is submitted awaiting processing. This SRA will be released on 2026-01-01 or upon publication.
