How I can get the UMI extraction file

Question

[yueli7]

Hello,

I followed the https://umi-tools.readthedocs.io/en/latest/QUICK_START.html.

Right now, I have files:

processed.fastq.gz, example.bam, example.bam.bai, deduplicated.bam, deduplicated_edit_distance.tsv, deduplicated_per_umi.tsv, deduplicated_per_umi_per_position.tsv.

How I can get the UMI extraction file?

Thanks in advance!

Best,

Yue

UMI extraction file:

@HISEQ:87:00000000_GGTT read1
TGATTGGATGGGCTAG
1AFGGCG01DFH00B1FF0B
+

[i.sudbery]

The file you are showing is the contents of processed.fastq.gz.

processed.fastq.gz is the result of extracting the UMIs from example.fastq.gz

[yueli7]

Hello, i.sudbery,

Thank you so much for your quick response!

The format of the processed.fastq does not look like barcode file.

Thank yo again!

Best,

Yue

li@li-HP-Pavilion-Desktop-590-p0xxx:~$ head -n 20 example.fastq
@SRR2057595.7
CAGGTTCAATCTCGGTGGGACCTC
+SRR2057595.7
1=DFFFFHHHHHJJJFGIJIJJIJ
@SRR2057595.9
TTGGTTCAATCTGATGCCCTCTTCTGGTGCATCTGAAGACAGCTACAGTGTACTTAGATATAATAAATAAATCTT
+SRR2057595.9
4=DFDBDHHFHHIGGEHJGGIHGHGGCAFCHGIGEHIJJJJIJJJIHIIIIIIJIIIIIGHIIGGIJGIIJIIJ@
@SRR2057595.14
TGGGTTAATGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT
+SRR2057595.14
1=DFFFFHHHHHJJIJJJJIGHJJIIJJJJJIJHFHHFFEDEEEEDDDDBDDDD
@SRR2057595.22
ACGGTTAATGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC
+SRR2057595.22
1=DFFFFHHHHHJJJJJJJJIJJJJJJJJJJJJHHHFFFEDEEEEDDDDBDDD
@SRR2057595.23
GCGGTTATTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAAAAGCTCGCTTGATCT
+SRR2057595.23
1=DFFFFHHHHHJJJJJJJJJJJJJJJIJJIIJJJJJJJJJJJJIJJHHHHHFFFFDDDDDDDDDDDDDDDDDDA


li@li-HP-Pavilion-Desktop-590-p0xxx:~$ head -n 20 processed.fastq
@SRR2057595.7_CAGGTTCAA
TCTCGGTGGGACCTC
+
HHHJJJFGIJIJJIJ
@SRR2057595.9_TTGGTTCAA
TCTGATGCCCTCTTCTGGTGCATCTGAAGACAGCTACAGTGTACTTAGATATAATAAATAAATCTT
+
FHHIGGEHJGGIHGHGGCAFCHGIGEHIJJJJIJJJIHIIIIIIJIIIIIGHIIGGIJGIIJIIJ@
@SRR2057595.14_TGGGTTAAT
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT
+
HHHJJIJJJJIGHJJIIJJJJJIJHFHHFFEDEEEEDDDDBDDDD
@SRR2057595.22_ACGGTTAAT
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC
+
HHHJJJJJJJJIJJJJJJJJJJJJHHHFFFEDEEEEDDDDBDDD
@SRR2057595.23_GCGGTTATT
CCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAAAAGCTCGCTTGATCT
+
HHHJJJJJJJJJJJJJJJIJJIIJJJJJJJJJJJJIJJHHHHHFFFFDDDDDDDDDDDDDDDDDDA