Muhammad Arshad

Thank you so much for your quick response. What you said totally makes sense so I would go with the second option that you mentioned. I am going to run...

Hello jtamames, As you suggested, I completed the full squeezemeta pipeline until the end using -extassembly. Here is the command: `SqueezeMeta.pl -m coassembly -p mangrove -s envi.samples -f clean_reads -extassembly...

Last two lines look like this: `Consensus: Total size: 692458 Disparity: 0.000 List of taxa (abundance >= 1%): k:;p:;c:;o:;f:;g:;s:;` Please see attached the syslog file. Seems like this is from...

Yes, I performed the external binning using this same megahit/final_assembly.fasta assembly. Only difference is that I obtained about 70 bins in total with external binning approach and provided only 17...

Here it is: Command: grep ">" 01.mangrove.fasta | head (in the results directory) Output: `>megahit_1 >megahit_2 >megahit_3 >megahit_4 >megahit_5 >megahit_6 >megahit_7 >megahit_8 >megahit_9 >megahit_10` Command: head bin10.fa.tax (in the results/bin...

Names of contigs in the assembly and contigs in bins do look different, as you predicted. How can we fix this please?

Ok, thank you sooo much. Now running it again and added --norename to the existing script. Will update you on this after run finishes. Many thanks again!

Yes, the above command (grep ">" results/01.mangrove.fasta | head) produces these headers: >k119_1895242_length_219358_cov_33.0684 >k119_284560_length_174923_cov_34.3021 >k119_264955_length_165023_cov_36.8075 >k119_1124181_length_158402_cov_32.8365 >k119_93162_length_151822_cov_33.5871 >k119_74209_length_150713_cov_22.9741 >k119_704680_length_148697_cov_241.8619 >k119_1806072_length_141893_cov_26.9927 >k119_334843_length_138599_cov_32.9593 >k119_877772_length_137089_cov_18.0030 That means it's not changing names so it...

Ok, the run has completed and then I submitted the `restart.pl -step 16 mangrove` and that has also completed successfully. Now I have all the required tables, I believe. Next,...

Dear @jtamames Hope you're doing well. Could you please let me know how can I calculate the gene abundance in each genome? Next, what I did is that I ran...