User: rbronste
rbronste • 160
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Posts by rbronste
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... Currently if getting a fimo database for specific TFs can do the following:
fimo -max-stored-scores 10000000 --thresh 1e-6 -oc /path/to/output/directory -motif /path/to/motif/file \
/path/to/HOCOMOCOv11_HUMAN_mono_meme_format.meme /path/to/whole_genome.fa
Is there a good way to do this f ...
written 8 days ago by
rbronste • 160
• updated
8 days ago by
Alex Reynolds ♦ 23k
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... Actually when I pull one specific sequence out of the -db input and run a blast on that against gapdh it works however when its many added sequences in the -db input against the -query it gives me this error.
...
written 4 weeks ago by
rbronste • 160
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... >flattened_line_0
GGGGGTTTTATAATTGTTGCTTTGACTCTGGCCCTGTGCAGCTCCTCCTCTGCTGCCCCGGTGGAGTCCTTTTACCCTCCAAGTTCTGCTGGAGCAGGCCCAGCAAGCCTCGCTCTGGTGGTTTTGGTCCCCTCTGGAAGAAGGGGGTGGGAGGGGCAGGCTGGTGGCTGGAGGAGAAAAGGGATGCGGGTGTGCTAGGGAGCAGGTGATGCAGAGATGGTGAAGTGGCATTGGGAGATGGAGTGTTTAAATGTTAAGGGGTGGGTAGAAA ...
written 4 weeks ago by
rbronste • 160
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... Building a new DB, current time: 04/19/2018 16:29:25
New DB name: a.lines.fasta
New DB title: a.lines
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 947804 sequences in 86.6696 seconds. ...
written 4 weeks ago by
rbronste • 160
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... I was actually just using the blast that was installed as a module on our computing cluster but yes it is quite aged. I guess I can install my own copy. ...
written 4 weeks ago by
rbronste • 160
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... Yes one did have spaces, got rid of those however the second error still persists. ...
written 4 weeks ago by
rbronste • 160
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... Wondering why I am getting following error, building the database as follows:
makeblastdb -in a.lines.fasta -input_type fasta -title a.lines -parse_seqids -dbtype nucl -out a.lines.fasta
After this running the following command:
blastn -db a.lines.fasta -query gapdh_mus.fa
Error:
Er ...
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... So I am using FIMO on some small datasets to look for motifs of interest and it works quite well to scan a PWM against some fasta file I chose, however the result basically outputs something like the following:
MA0041.1 Foxd3 chr1:146119062-146119793 + 24 35 2.03e-07 0.0191 GATTGTTTGTTT
MA0 ...
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Comment:
C: FIMO output to bed
... Your command just pulls out the factor name instead of the interval, seems like the current format for FIMO output is a little different - can you suggest on how to adjust? Thanks!:
# motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence
MA0032.2 FOXC ...
written 5 weeks ago by
rbronste • 160
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... So you would just subsample at different % until it hits around the size of the other BAM files or is there another downstream metric? ...
written 8 weeks ago by
rbronste • 160
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