how to use ICRA to calculate microbial abundances

[Yingli Zhou]

Dear developer,
I use this command python /data2017/zhouyl/software/SGVFinder-master/src/ICRA_cmd.py /data2017/zhouyl/test/svgtest/result /dataNew/User/zhouyl/sediment/TS01_LD10/CLEAN_READS/TS01-LD10-1 --pe --use_theta to run ICRA. There are two output files TS01-LD10-1.jsdel and TS01-LD10-1.pmp. ICRA seems work now. But where should I input my genomes to calculate microbial abundances of my metagenome.
Thanks in advance.

[David Zeevi]

Dear user,
We do not support microbial abundance calculations in ICRA. Should you want to pursue this, you may sum up the reads mapped to each genomic element in the .jsdel file and divide by the total sum.

[Yingli Zhou]

We do not support microbial abundance calculations in ICRA. Should you want to pursue this, you may sum up the reads mapped to each genomic element in the .jsdel file and divide by the total sum.

Hi @davidzeevi, thanks for your reply.
I want to calculate microbial abundance by ICRA. Can you introduce the file format to me. The following is the .jsdel file output by my data [["M03609:19:000000000-AHFUY:1:1101:18854:2700",[["1298885.PRJNA190793",890101,890330,1,1]]]
But I only import pair-end fastq files in ICRA . How can I import genome from binning of my metagenome.
Thanks

[Yingli Zhou]

Hi @talkr
Running SGVF_PerFile_cmd.py needs three arguments ：
1、deltaf （Is the .jsdel file from the ICRA?）
2、outf （I know it is the output file name）
3、average_read_length （What should I input？）
I don't know how to input these arguments. Can you give me some help? Thanks

[talkr]

1. yes.
2. The average read length in your original fastq file. Will usually be 75 or 100.