Questions tagged [bioawk]
For questions about bioawk, an extension of the unix core utility command awk.
11
questions
4
votes
1
answer
320
views
Find pattern that is present twice and allow <=2 mismatches on each
I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...
- 69
1
vote
1
answer
55
views
how to repeat records in fastq n times efficiently?
How to iterate/repeat a record n times in a fastq file using bioawk? I wrote a python code using biopython, but it is very very slow. So, I am wondering if I can get some help by using bioawk. Thank ...
- 13
6
votes
5
answers
2k
views
Delete all 4 lines of a fastq read from a fastq file using read ID
I have the following error when running bowtie2:
Error: Read HWI-D00466:116:CC62WANXX:3:1102:7363:63646 1:N:0:GCACACG
has more read characters than quality values.
I now want to remove all 4 ...
- 61
2
votes
2
answers
695
views
filter out FASTQ reads which are shorter
I tried to filter out FASTQ reads which are shorter than 259 bp with
...
- 275
4
votes
1
answer
153
views
bioawk removed part of FASTQ header
I used
bioawk -cfastx 'length($seq) > 1 {print "@"$name"\n"$seq"\n+\n"$qual}' in.fq.qz | gzip > out.fq.qz
in order to keep a particular read length, but ...
- 453
4
votes
2
answers
9k
views
Calculating read average length in a Fastq file with bioawk/awk
I found here this awk script:
...
- 453
2
votes
1
answer
98
views
Splitting characters of a column in repeated lines and reducing them to one line
I have a file with sample data like this:
...
- 353
4
votes
1
answer
88
views
Intersecting two different files with one "master" file based on different columns
I have the following sets of data:
file1:
1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 16855676 16855696 CTGTCCAGCAGAGGGCGGTG
file2:
...
- 353
4
votes
2
answers
165
views
Using column 2 of one file to match with two columns of another file, and append
I have file 1 like following:
1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 16855676 16855696 CTGTCCAGCAGAGGGCGGTG
And file 2 as following
...
- 353
10
votes
3
answers
2k
views
Selecting sites from VCF which have an alt AD > 10
I have high-depth variant calling created using the HaplotypeCaller with --output_mode EMIT_ALL_SITES I'm interested in finding all sites (regardless of genotype ...
- 1,059
4
votes
1
answer
339
views
What kind of "gff" format does bioawk parse?
I was wondering if I could use the gff parsing capability of bioawk to facilitate the parsing of gtf files, and I looked at the following help message:
...
- 3,100