lpantano
commented
6 months ago Hi, I see the problem, it seems they stopped supporting that file. I would recommend to use STAR or bowtie to map reads to precursors and then use mirtop to parse the output and get isomir annotation.
bowtie \\
-x \$INDEX \\
-q <(zcat $reads) \\
-p ${task.cpus} \\
-t \\
-k 50 \\
--best \\
--strata \\
-e 99999 \\
--chunkmbs 2048 \\
--un ${meta.id}_unmapped.fq -S > ${meta.id}.samon another note you can use: https://nf-co.re/smrnaseq/2.2.4 to analyze everything and it will generate a lof results for this type of data.
Alarabi1980
Hi Lorena,
Hope this email finds you well,
I am working on miRNA seq data, and I am using your pipeline https://seqcluster.readthedocs.io/mirna_annotation.html to find Isomirs, but I am faced with some difficulties as the final output show me no results. so, I was wondering if I am making a mistake or something. one of the issues if in the pipeline page one of the file needed is miRNA.str? which I am supposed to download from mirbase. but there is not such file the only file available is mature.fa file is this the same? but when I use this file, it gives me an error that I am missing miRNA.str file? so, I changed the mature.fa file to mature.str and it worked with no error but no results?
can you please help me
Thanks
command (bcbio) ahmed@ahmed-Precision-5570:~$ java -jar /home/ahmed/tools/miraligner.jar -sub 1 -trim 3 -add 3 -s mmu -i /home/ahmed/data/PEHmiRNA/collapse/trimmed_001.R1_trimmed.fastq -db /home/ahmed/data/PEHmiRNA/DB -o /home/ahmed/data/PEHmiRNA/collapse/output_prefix Format is not tabular,guessing fasta species found Go to mapping... Mismatches: 1 Trimming: 3 Addition: 3 Species: mmu Feb 20, 2024 2:02:32 PM miraligner.map readseq INFO: Tue Feb 20 14:02:32 EST 2024
Feb 20, 2024 2:02:32 PM miraligner.map readseq INFO: Tue Feb 20 14:02:32 EST 2024
Reading reads Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Number of reads excluded because size: 590697 Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Number of reads excluded because size: 590697 Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Number of reads to be mapped: 154078 Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Number of reads to be mapped: 154078 Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Searching in precursors Feb 20, 2024 2:02:33 PM miraligner.map readseq INFO: Searching in precursors Feb 20, 2024 2:02:36 PM miraligner.map readseq INFO: Tue Feb 20 14:02:36 EST 2024 Feb 20, 2024 2:02:36 PM miraligner.map readseq INFO: Tue Feb 20 14:02:36 EST 2024 Feb 20, 2024 2:02:36 PM miraligner.map readseq INFO: Num reads annotated: 38720 Feb 20, 2024 2:02:36 PM miraligner.map readseq INFO: Num reads annotated: 38720