Hi I am using Megan 6.8.19 and i am trying to extract reads from a node using extra. However, the output fasta file only contains fasta headers like
M02023:25:000000000-A6UEU:1:1101:15447:1432
M02023:25:000000000-A6UEU:1:1101:14258:1980
M02023:25:000000000-A6UEU:1:1101:13831:2159
M02023:25:000000000-A6UEU:1:1101:18894:2652
M02023:25:000000000-A6UEU:1:1101:12552:2673
Do you know why this could happen
thanks
adela
Does you MEGAN file contain the reads? To check, open any node in the Inspector window. Then inspect the Data item of some read in the inspector window. If there is no sequence there then that means that you did not import the reads when you created the MEGAN file. If there is sequence present, then please let me know exactly which command you used to extract reads.
Hey Adelujan,
I encountered the same problem. Our NGS device produces headers of this type:
“>@somestring someotherstringafterspace”
I used this fasta file for the blast search. But after that, the string after the space gets lost. This is the first part of the problem.
If I import this fasta file, I also get just the headers when trying to export reads. But they look different:
“>somestring”
I guess MEGAN6 processes this header by removing the “@” . This is the second part of the problem, because now of course MEGAN6 cannot match the headers with the ones of the fasta file.
Long story short: Make sure that your headers are (at the earliest step possible) without any special characters and spaces.
Hope this could help.
Yes, sorry, anything past the first space is removed (to save space) and MEGAN assumes that the word before the first space is a unique identifier.
Not sure why the @ is lost, I will try to look into this