burkholderab
commented
4 years ago Hi Marius,
Muver was designed to work with Illumina sequencing data, which is typically delivered in FASTQ format. If you have next generation sequencing reads in FASTA format, the pipeline can be run manually, however, the process is lengthy, and requires some commands be run with specific parameters to maintain compatibility with downstream steps. If you are able to install the package from github rather than utilizing the docker container, a minor modification of this file, https://github.com/NIEHS/muver/raw/master/muver/wrappers/bowtie2.py, can add support for FASTA input. Simply change the parameter on line 34 from '-q' to '-f', which indicates that the aligner, bowtie2, should expect FASTA rather than FASTQ input. When you generate the “FASTQ_list” file, you can include just the “Mate 1 FASTQ” column, just as you would with single-end FASTQ input, but list the names of your FASTA files instead.
You may be able to replace the original with an updated copy within the docker container by specifying ‘-u 0’ in the run command to enter the shell as root. The file to be replaced is:
/usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg/muver/wrappers/bowtie2.py
…and you can place the modified copy in your mounted data directory.
I was able perform the modification successfully on two different Linux-based docker environments, however, depending on how your system is configured, this approach may not work for you.
Thanks,
Adam
From: Marius Gheorghe notifications@github.com Sent: Tuesday, March 31, 2020 8:43 AM To: NIEHS/muver muver@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [NIEHS/muver] run muver on FASTA instead of FASTQ (#6)
Hi,
Was wondering if it is possible to run muver starting from FASTA files instead of FASTQ file. I see that the run_pipeline requires the FASTQ_list with mate 1 and 2 columns, information that I do not have.
Please let me know. Thank you in advance!
Marius
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/NIEHS/muver/issues/6, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADCMIB2FBF3RUCOD2ZDJZP3RKHQL3ANCNFSM4LXQQ2TA.
MariusGheorghe
Hi,
Was wondering if it is possible to run muver starting from FASTA files instead of FASTQ file. I see that the
run_pipelinerequires theFASTQ_listwith mate 1 and 2 columns, information that I do not have.Please let me know. Thank you in advance!
Marius