User: RT

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RT280
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280
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European Union
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4 hours ago
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Posts by RT

<prev • 133 results • page 1 of 14 • next >
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meme-suite: How does FIMO works?
... Dear All, I am new to motif identification area. From a set of sequences (~200), I want to search for a known motif and filter out sequences where the motif does not exist. My motif is 8bp long. A simple python search gave me too many random hits. Someone quickly suggested to me to use meme-tools a ...
meme-suite motif identification fimo written 9 days ago by RT280
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pybedtools change fasta headers
... I am using pybedtools to get promoter sequences for my genes of interest. I am almost done with the script. But I would also like to include gene names in the fasta headers. By default, it only include corrdinates in fasta headers. Below is my script: >coords=Chr1 1000 2000 forward 1 + >a ...
python pybedtools written 19 days ago by RT280
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Chip-seq on pooled replicates
... Dear All, Can someone please help me to understand why for ChIP-seq we should not merge the biological replicates before peak calling. I read in several papers, peaks calling is done on individual replicates. I am struggling to understand this. Ideally if I merge replicates I should have more power ...
chip-seq pooled replicates written 4 weeks ago by RT280 • updated 4 weeks ago by EagleEye3.4k
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Comment: C: Macs2 failed for pooled samples
... I am very confused now. I actually started following IDR pipeline. Does not it recommend to run macs2 on both individual replicates and pooled replicates? https://sites.google.com/site/anshulkundaje/projects/idr ...
written 5 weeks ago by RT280
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macs2 warnings unknown sequencing problem
... Hi All, I have chipseq single-end reads of length 130 bp. From macs2 output I got the warning 'Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!'. Can it be because macs2 is not estimating the fragment length correctly ...
chipseq macs2 single end data written 5 weeks ago by RT280
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Macs2 failed for pooled samples
... Dear All, I am new to ChIP analysis. I have 3 replicates for ChIP samples and 2 for control samples. I am using macs2 for peak calling. It was all going well until I called peaks on pooled replicates. MACS2 command: macs2 callpeak -t chipdata_pooled.tagAlign.gz -c mocksamples.tagAlign.gz -f B ...
macs2 chip-seq written 5 weeks ago by RT280 • updated 5 weeks ago by EagleEye3.4k
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samtools flag 1548
... Hi all, Just a quick question- can somebody please explain to me what is the meaning of 1548 in the following samtools command: samtools view -b -F 1548 Thanks, RT ...
bitwise flags samtools written 6 weeks ago by RT280 • updated 6 weeks ago by Pierre Lindenbaum91k
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Literature mining based on gene annotation
... Dear All, I was wondering if it is possible to mine the published studies for a species based on their gene annotation. For example, if I want all the transcriptome studies for human transcription factors. Is it possible to make this kind of queries on some database? Currently I am making the foll ...
data-mining annotations written 10 weeks ago by RT280 • updated 10 weeks ago by natasha.sernova2.4k
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Comment: C: Implementing McDonald-Kreitman test
... I end up using python egglib library for this... ...
written 3 months ago by RT280
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Comment: C: Identification of network root and building parent child relationship
... Hi Jaime, I have cyclic network. Is there any way to do this for cyclic networks? ...
written 8 months ago by RT280

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