no annotaion file output

[xingchang-web]

Hi Junchao, I used this command line to annotate small RNA(input file is fastq format): sports.pl -i seq_address.txt -p 4 -g /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/genome/hg38/genome \ -m /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/miRBase/21/miRBase_21-hsa \ -r /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/rRNAdb/human_rRNA \ -t /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/GtRNAdb/hg19/hg19-tRNAs \ -w /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/piRBase/piR_human \ -e /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/Ensembl/release-89/Homo_sapiens.GRCh38.ncrna \ -f /BIGDATA2/sysu_hshwang_1/soft/database/Homo_sapiens/Rfam/12.3/Rfam-12.3-human \ -o /BIGDATA2/sysu_hshwang_1/sports/output the output file is follow:

There is no error in the log file:

[junchaoshi]

Hi,

May I have the headline of the .fq file?

Junchao

[xingchang-web]

The headline of input .fq file as follow:

[junchaoshi]

Hi,

The 5' and 3' adaptors need to be removed using the -a -x -y parameters in SPORTS.

Best, Junchao

[xingchang-web]

Hi Junchao, Thanks for your answer. Can i use sports to annotate tRF for miRNA-seq in TCGA? Best, xingchang

[junchaoshi]

Hi Xingchang,

Yes, you can! However, it's worth noting that traditional small RNA-seq methods have limitations when it comes to detecting tsRNAs due to the obscurity of RNA modifications (I have screened the data in TCGA before). We highly recommend reading our research papers for more in-depth information on this subject: https://www.nature.com/articles/s41556-021-00652-7 and https://www.nature.com/articles/s41556-022-00880-5.

Best, Junchao