Thanks a lot, it works
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Extract sequences from a fastq file by a list of IDs
Hey guys,
I have a fastq file looks like this:
@E100062344L1C001R00100004672/1
TGGCCATTTTCCGAAAGAACGAGTGCTTTTATATTTGAAACGCTCGGATAGTCAGTGTAC
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6C?;?F@DFD?F:<FB>FEFF3?EFCEEEDFDF;EFE5EFB88C9@0F9EDF9F7;EFED
@E100062344L1C001R00100007908/1
TTATACAACGTTTTCAAAGTATCAAAATACGTATTAACTTATTTTCATTAATATTATGTTGTTGTTTTTTTTTTAAATT
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EGGFGDF<DFFBFGGFFFGFFF9FFFF3FFFEFFFGFDFDFF?GFFG6GGFDFGCBFFDFGDFE@FGFGFGGBFB@F>F
@E100062344L1C001R00100042396/1
AGCTAGTTAGCAAACTCACATTGGTTTTCAAAATTCCAACACCTTTTGGTAGAAGAAAA
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FFFFGF@3FFFFF;BDGGFDEGEFBFFCGGFFGFGFCDFFFGC@FECF<FFF?<EFGF?
@E100062344L1C001R00100052634/1
CAGCAGAAGCAGACGCCAGAAGAACGGCCAAGGAAGATAAGATTCGTGGTGAACTCACCG
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FC.=A0E*B8:<51F66A3<E58/8C<ECE;==0EFC@EA6EFCCA+5@E+1F:A6@CCC
and also I have IDs file that looks like this:
E100062344L1C001R00100004672
E100062344L1C001R00100007908
I am trying to extract for my fastq file the sequences that have their id in my txt.file. I am using seqkit for that, but with no success. Do you have any idea that how can I extract the sequences of my IDs?
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Ram
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mhpakdel96 •
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mhpakdel96 •
2 answers
Using filterbyname.sh from BBMap suite:
You need to include the /1 in the header in your list file (here I am using the name=your_header_example directly but names=file_w_names, this file will contain one ID per line). This is likely your problem when you say "you tried them all but none work".
$ filterbyname.sh in=test.fq out=stdout.fq names=E100062344L1C001R00100007908/1 include=t
Or use substring=t option (no need to add /1 at end)
$ filterbyname.sh in=test.fq out=stdout.fq names=E100062344L1C001R00100007908 substring=t include=t
Both will get you the following output.
Input is being processed as unpaired
@E100062344L1C001R00100007908/1
TTATACAACGTTTTCAAAGTATCAAAATACGTATTAACTTATTTTCATTAATATTATGTTGTTGTTTTTTTTTTAAATT
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EGGFGDF<DFFBFGGFFFGFFF9FFFF3FFFEFFFGFDFDFF?GFFG6GGFDFGCBFFDFGDFE@FGFGFGGBFB@F>F
Time: 0.196 seconds.
Reads Processed: 4 0.02k reads/sec
Bases Processed: 258 0.00m bases/sec
Reads Out: 1
Bases Out: 79
Replace stdout.fq (I was writing to screen in this example) with a filename to get file output. You can use gzipped files directly as input and output.
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
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why screenshots when you can just copy and paste the text ? How To Extract Set Of Reads From Fastq (Or Eventually Fasta And Qual) Based On List Of Ids? extracting reads from fastq file based on read_id How To Extract A Subset Of Reads In Fastq Using An Id List? Extracting specific sequences from FASTQ using Seqtk choosing reads from a fastq file based on another fastq file etc....
I have tried all of them but none of them work for me
https://meta.stackexchange.com/questions/147616/