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wejlab / MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)
GNU General Public License v3.0
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metascope for assembled contig? #26

Closed esraagithub closed 7 months ago

esraagithub commented 7 months ago

hello can i use metascope for assembled contigs?

aubreyodom commented 7 months ago

Hi,

If the assembled contigs are in FASTA format, then you would be able to align these if you include "-f" in the bowtie2_options parameter in the align_target_bowtie() function.

esraagithub commented 7 months ago

Is there similar option in subread?

في الأحد، ٤ فبراير ٢٠٢٤ ٨:٠٩ م Aubrey Odom @.***> كتب:

Hi,

If the assembled contigs are in FASTA format, then you would be able to align these if you include "-f" in the bowtie2_options parameter in the align_target_bowtie() function.

— Reply to this email directly, view it on GitHub https://github.com/wejlab/MetaScope/issues/26#issuecomment-1925868611, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMY4XZWXFF7KVDWE5ODZJC3YR7FFNAVCNFSM6AAAAABCYSFRECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVHA3DQNRRGE . You are receiving this because you authored the thread.Message ID: @.***>

aubreyodom commented 7 months ago

According to the documentation for Rsubread::align():

input_format | character string specifying format of read input files. gzFASTQ by default (this also includes FASTQ, FASTA, gzipped FASTQ and gzipped FASTA formats). Other supported formats include SAM and BAM. Character values are case insensitive.

So you would use something like c("input_format" = "FASTA") or append to the MetaScope align_details object to pass to MetaScope::align_target.