Forward reads appear to not be of consistent length

[BirongZhang]

Hi figaro team,

Thanks for developing such a wonderful tool！

But I have some problem when I use it. I have 22 paired data(515FB and 926R ), each one is close to 300bp. I used figaro before trimming the primers.

1. python3 $FIGARO_HOME/figaro.py -i data2 -o figaro -a 300 -f 19 -r 20 -F illumina

   

2. Then I use FASTX-Toolkit to trim them at the same length: for i in data2/*.fastq do fastx_trimmer -f 5 -l 295 -i $i -o data3/$i done

3. python3 $FIGARO_HOME/figaro.py -i data3/data2 -o figaro -a 300 -f 19 -r 20 -F illumina

   

So what is the problem with my script? I would appreciate any suggestions, thanks!

Kind regards, Birong

[michael-weinstein]

This looks interesting. I think FIGARO is detecting the reads as still having some variability in length… maybe you had a few short ones in there. Try trimming down to 290 and let me know what happens.

From: BirongZhang @.> Sent: Wednesday, June 9, 2021 9:39 AM To: Zymo-Research/figaro @.> Cc: Subscribed @.***> Subject: [Zymo-Research/figaro] Forward reads appear to not be of consistent length (#38)

Hi figaro team,

Thanks for developing such a wonderful tool！

But I have some problem when I use it. I have 22 paired data(515FB and 926R ), each one is close to 300bp. I used figaro before trimming the primers.

1. python3 $FIGARO_HOME/figaro.py -i data2 -o figaro -a 300 -f 19 -r 20 -F illumina

   https://user-images.githubusercontent.com/74430395/121393820-a0f26300-c948-11eb-8952-baa362aec310.png

2. Then I use FASTX-Toolkit to trim them at the same length: for i in data2/*.fastq do fastx_trimmer -f 5 -l 295 -i $i -o data3/$i done

3. python3 $FIGARO_HOME/figaro.py -i data3/data2 -o figaro -a 300 -f 19 -r 20 -F illumina

   https://user-images.githubusercontent.com/74430395/121394014-d5feb580-c948-11eb-8346-f16fc77de670.png

So what is the problem with my script? I would appreciate any suggestions, thanks!

Kind regards, Birong

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[BirongZhang]

Hi Michael,

Thanks for your efficient reply and kind help!

Yes, you are right. I tried to trim them down to 290, and this time the above error did not occur. However, there is a new error.

1. for i in data2/*.fastq do fastx_trimmer -f 5 -l 290 -i $i -o data3/$i done
2. python3 $FIGARO_HOME/figaro.py -i data3/data2 -o figaro -a 290 -f 14 -r 10 -F illumina

I am looking forward to hearing form you, many thanks！

Birong

[michael-weinstein]

How long is your amplicon? Is it only 300 bases?

Sent from my iPhone

On Jun 9, 2021, at 2:31 PM, BirongZhang @.***> wrote:

 Hi Michael,

Thanks for your efficient reply and kind help!

Yes, you are right. I tried to trim them down to 290, and this time the above error did not occur. However, there is a new error.

for i in data2/*.fastq do fastx_trimmer -f 5 -l 290 -i $i -o data3/$i done python3 $FIGARO_HOME/figaro.py -i data3/data2 -o figaro -a 290 -f 14 -r 10 -F illumina

I am looking forward to hearing form you, many thanks！

Birong

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[BirongZhang]

Yes, each one is close to 300bp. Here is the quality plot, hope it helps. Thanks!

[LiaOb21]

Hi Michael, I started from a practically equal situation to the one reported by BirongZhang. I decided to trim the reads because FIGARO doesn't support variable lengths. I was still having errors, so I followed your suggestion of trimming up to 290. The first error ("reads appear to not be of consistent length") seems to be solved, but I run into the same last error that BirongZhang reported:

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (29971,) + inhomogeneous part.

Any idea on how solve that? Thank you so much in advance!

[jpmgzmn]

Hi all! Thanks to this thread, the issue about variable sequence lengths was resolved. However, I've encountered exactly the same issue just now about ValueError. Specifically, I got this error too:

ValueError: setting an array element with a sequence.

Has anyone resolved this since? Thank you so much!