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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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why ShortStack is not recognizng input raw read file? #77

Closed Ashar14 closed 3 years ago

Ashar14 commented 6 years ago

Hello, I am trying to analyse my small RNA seq data for the miRNA prediction. I installed the ShaortstacK and the required dependencies. I a providing the input file and the bam alignment file (already aligned separately) bu shortStack is giving the following error message: the code I ran tb44227@lido-gw01:~/nobackup/PROJECTS/01_C.Sativa/sRNA_seq/4_BWT_mapping>~/bioinfo_packages/ShortStack-3.8.5/ShortStack -outdir ../5_Short_Stack_out/ --readfile 754_1-15.fastq.gz -bamfile 754_1-15.bam --genomefile 2271-94_concat_Trinity.fasta

Error message: Invalid option combination: readfile is mutually exclusive with bamfile and/or cramfile

MikeAxtell commented 6 years ago

Hello, thanks for your message. Option --readfile lets you specify one or more fasta/fastq files that are to be aligned. In contrast, option --bamifle lets you specify a pre-existing alignment file (in bam format) to analyze. You can't specify both at the same time. Note that --bamfile is not a specifier for an output file name.

Hope this helps, Mike

On Mon, Jul 9, 2018 at 4:59 AM Ashar14 notifications@github.com wrote:

Hello, I am trying to analyse my small RNA seq data for the miRNA prediction. I installed the Shaort stacj and the required dependencies.I a providing the input file and the bam aignment file (already aligned separately) bu shortStack is giving the following error message: the code I ran tb44227@lido-gw01:~/nobackup/PROJECTS/01_C.Sativa/sRNA_seq/4_BWT_mapping>~/bioinfo_packages/ShortStack-3.8.5/ShortStack -outdir ../5_Short_Stack_out/ --readfile 754_1-15.fastq.gz -bamfile 754_1-15.bam --genomefile 2271-94_concat_Trinity.fasta

Error message: Invalid option combination: readfile is mutually exclusive with bamfile and/or cramfile

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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell

Ashar14 commented 6 years ago

Thanks. I got it.

Another thing I would like to ask whether it possible to resume Shortstack?

MikeAxtell commented 6 years ago

Resume ? I don't know what you mean. But if you mean something like re-starting a suspended job, then no.

On Tue, Jul 10, 2018 at 6:09 AM Ashar14 notifications@github.com wrote:

Thanks. I got it.

Another thing I would like to ask whether it possible to resume Shortstack?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MikeAxtell/ShortStack/issues/77#issuecomment-403771370, or mute the thread https://github.com/notifications/unsubscribe-auth/AGiXiaRX1dH1cPzkfrLopWcpnBNTGvM0ks5uFH05gaJpZM4VHVFz .

-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell