Seqlogo generation and interpretation
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2.1 years ago
jaqx008 ▴ 110

seqlogo -F pdf -C 13 -c -S -B 2 -f male.13.fa -o seqlogo13.pdf

hello everyone. below (link1) is a seqlogo I generated using the command above. I am trying to interprete the image with regards to reads that begin with either a G or an A on the 5' end. I dont know what to deduce from this image since the first and second lines dont begin with either G or A. Can someone help? Also, I want to make a seqlogo figure like bellow (link2) but the command keep complaining about uneven length when i set the length to be anything above 13. Does anyone know how I can get the image bellow since I have the same seq data to make it? A recommendation of how I can interprete it would also be helpful.

for first figure I only provided a fasta file

>1-5183
TAGACTCCGACAC
>2-2196
TCGCAGACACCGA
>3-1786
TGACGTCGTAGAC
>4-1406
TGTCGTCGCAGAC
>5-1178
TAGACTCCGATAC
>6-1127
TAGACTCCGACAC


in attempt o make second figure, I supplied seqlogo with a fasta file containing all reads up to 20, 21, 22, 23 ... 30. hope this helps

seqlogo 5' ID polymerase • 438 views
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show us the nucleotide matrix you fed seqlogo

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for first figure I only provided a fasta file

>1-5183
TAGACTCCGACAC
>2-2196
TCGCAGACACCGA
>3-1786
TGACGTCGTAGAC
>4-1406
TGTCGTCGCAGAC
>5-1178
TAGACTCCGATAC
>6-1127
TAGACTCCGACAC


in attempt o make second figure, I supplied seqlogo with a fasta file containing all reads up to 20, 21, 22, 23 ... 30. hope this helps

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2.1 years ago

This is what I got using seqlogo from weblogo.2.8.2 your fasta file. Could you be just looking at the wrong output file from a previous run?

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what I pasted was actually a small portion of the fasta file. However, I see now that seq logo gives that were as weblogo gives close to what I am looking for. Thanks alot

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in this case seqlogo is just the CLI version of weblogo. they should be identical given the same parameters and input.