Trinity, longest contigs

Question

[loly.pearl86]

Hi All,

Can some one explain to me how can I generate the longest and shortest contigs length from this trinity assembly summary:

################################
## Counts of transcripts, etc.
################################
Total trinity 'genes': 306290
Total trinity transcripts: 369174
Percent GC: 48.47

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 5172
Contig N20: 3581
Contig N30: 2517
Contig N40: 1717
Contig N50: 1095

Median contig length: 333
Average contig: 659.77
Total assembled bases: 243568232

#####################################################
## Stats based on ONLY LONGEST ISOFORM per 'GENE':
#####################################################

Contig N10: 4276
Contig N20: 2665
Contig N30: 1655
Contig N40: 1006
Contig N50: 664

Median contig length: 313
Average contig: 540.34
Total assembled bases: 165499422

Thanks

Answer 1

[iraun]

There are a lot of ways to do this. If you want a command line fast solution, this one can deal with your issue:

awk 'BEGIN{RS = ">" ; ORS = ""}NR==2{ min=length($2); max=length($2); next} max < length($2) {max=length($2)} min > length($2) {min=length($2)} END {print "Shortest: "min"\nLongest: " max"\n"}' file

Basically you need to extract the length of each sequence, and save the highest and lowest value. As I told you, there are a plenty ways to do it, in different languages, or different tools. In my opinion awk is great for this kind of situations.

[loly.pearl86]

Thanks for u quick replay but I am not sure where can I run this script??! look like for Rstudio !! I am working on linux using (Putty) SSH. So can I run this script on SHH command line? If no, then can you please suggest to me other way which I can use it in linux

thanks

[iraun]

Yes. You can do it from the command line. Just move to the folder where your fasta file is located, and copy paste the command replacing file with your file name.

[loly.pearl86]

Thanks I did run it

its give me this result: shortest = 0 that is all !!

[iraun]

Sorry, I'd a little mistake. Can you try now?

[loly.pearl86]

Thanks its work now. But the results its unusual

I have 5 assembled samples , and the outcome of the script was

sample 1: shortest 1 longest 14357

Sample 2 , 3 ,4: shortest= 7 longest= 9

Sample 5 shortest=6 longest =89 Is this mean any things like my samples quality are poor or low quality??!!!

thanks