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Update Wolf tutorial with the OBITools3

Celine Mercier
2020-07-24 16:22:06 +02:00
parent f3176b77d1
commit 050d7c31cb
1 changed files with 5 additions and 1 deletions
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6
Wolf-tutorial-with-the-OBITools3.md

@ -49,6 +49,10 @@ And unzip it:
obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads obi alignpairedend -R wolf/reads2 wolf/reads1 wolf/aligned_reads
**Note:** For any command, you can also print the result to standard output using the `-` URI:
obi alignpairedend -R wolf/reads2 wolf/reads1 - > aligned_reads.fastq
### 3. Remove unaligned sequence records ### 3. Remove unaligned sequence records
obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences obi grep -a mode:alignment wolf/aligned_reads wolf/good_sequences
@ -57,7 +61,7 @@ And unzip it:
obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences obi ngsfilter -t wolf/ngsfile -u wolf/unidentified_sequences wolf/good_sequences wolf/identified_sequences
Note: Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads, BUT it is not recommended to do so for usual data, as ngsfilter will not be able to detect and cut out partially sequenced primers. **Note:** Unlike the OBITools1, the OBITools3 make it possible to run ngsfilter before aligning the paired-end reads, BUT it is not recommended to do so for usual data, as ngsfilter will not be able to detect and cut out partially sequenced primers.
### 5. Dereplicate reads into unique sequences ### 5. Dereplicate reads into unique sequences