Truncated read output

[jsthv]

When I try to simulate the ideal read for a 290 nt fasta inputfile the output signal file contains signals with variable length, i.e., 2380, 2230, 2070, 2710, 2580, 2260, 2250 points when there should be 2900 points. The original file I used was 145 nt, but the program will not take this short of a sequence, so I merely doubled it and found that variable amounts of the last part of the signal was missing.

[hasindu2008]

Hello

Could you please copy paste the commandline with parameters you used?

[jsthv]

Here it is:

CMD: squigulator -x dna-r10-min -o idealreadone2.slow5 -n 10 --ideal barcode1_54mer.fa

I then though that it might have to do with the fact that I used -n 10 instead of -n 1 as there should only be one ideal read but this one gave one read of only 1980 pts

If I omitted -n, I get a random collection of lengths just as with -n 10.

John

From: Hasindu Gamaarachchi @.> Sent: Wednesday, December 13, 2023 9:27 PM To: hasindu2008/squigulator @.> Cc: Taylor, John-Stephen @.>; Author @.> Subject: Re: [hasindu2008/squigulator] Truncated read output (Issue #7)

Hello

Could you please copy paste the commandline with parameters you used?

- Reply to this email directly, view it on GitHubhttps://github.com/hasindu2008/squigulator/issues/7#issuecomment-1855067915, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BEVIT5MVKQR5OWPUUYJH46DYJJWYVAVCNFSM6AAAAABAUAPNB2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGA3DOOJRGU. You are receiving this because you authored the thread.Message ID: @.**@.>>

[hasindu2008]

The command above treats the input sequence as a reference genome and sample reads from it. If you want the input sequence to be treated as a read, --full-contigs. I guess this is what you are after?