SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 15 of 15
Search took 0.00 seconds.
Search: Posts Made By: mparida
Forum: Bioinformatics 02-11-2017, 12:05 PM
Replies: 1
Views: 1,968
Posted By mparida
0 FPKM of genes with reads cufflinks

Hi All
I tried mapping my reads to the transcriptome instead of the genome and then computed the FPKM using eXpress algorithm (from the collaborating group that wrote cufflinks) and now my...
Forum: Bioinformatics 02-06-2017, 04:28 PM
Replies: 1
Views: 1,968
Posted By mparida
0 fpkm for genes with reads

Hi All
I have come across an issue of 0 fpkm even when there are reads for a locus.
I downloaded mm10 genome and annotation from https://ccb.jhu.edu/software/tophat/igenomes.shtml as recommended....
Forum: Bioinformatics 02-01-2017, 08:22 AM
Replies: 0
Views: 1,026
Posted By mparida
Amino acids premature stop codons

Hi All
I have downloaded Daphnia pulex amino acid sequence from wFleabase.
I found this amino acid sequence:
>hxNCBI_GNO_20744...
Forum: Bioinformatics 12-20-2016, 04:50 PM
Replies: 1
Views: 1,691
Posted By mparida
FIMO motif co-occurrences

For anyone who is interested I found a valid answer from Charles E Grant.
Biologically, a single site may bind to multiple transcription factors. In fact, the competition between TF for attachment...
Forum: Bioinformatics 12-19-2016, 12:11 PM
Replies: 1
Views: 1,691
Posted By mparida
Overlapping motif occurrences

Hi I am using FIMO to find all the significant+non-significant occurrences of a motif in a set of input sequences.
Sometimes I am getting an isolated motif occurrence and other times I am getting...
Forum: Bioinformatics 11-21-2016, 08:54 AM
Replies: 2
Views: 1,572
Posted By mparida
Thank you very much for your reply. Appreciate it.

Thank you very much for your reply. Appreciate it.
Forum: Bioinformatics 09-15-2016, 07:59 AM
Replies: 0
Views: 1,069
Posted By mparida
meme motifs

Hi
Is there a predefined way to pick number of motifs parameter in MEME?
By default meme may find only 1 motif according to the manual in my given set of sequences.
Rocky
Forum: Bioinformatics 09-12-2016, 09:51 AM
Replies: 2
Views: 1,572
Posted By mparida
MEME motif discovery

Hi
I have a question on meme motif discovery and strand of the sequence.
When discovering motifs does MEME considers by default both forward and reverse strands of a given input sequence? I read in...
Forum: Bioinformatics 11-06-2015, 03:34 PM
Replies: 1
Views: 1,056
Posted By mparida
GO analysis

Hi All
I am trying to choose between the following:
a) using all the genes in my genome as a background for my GO analysis
or
b) using only those genes that have at least 1 GO term as a...
Forum: Bioinformatics 07-10-2015, 07:57 AM
Replies: 1
Views: 1,092
Posted By mparida
Download UCSC genes and isoforms

Hi
I am trying to download dm3 2006,fruitfly genes and isoform track from UCSC. I have tried many different tracks on the Table browser but I still cannot get them isoform descriptions for all the...
Forum: Bioinformatics 12-29-2013, 08:43 AM
Replies: 9
Views: 8,266
Posted By mparida
Reply

Trimmomatic paramters:
-phred33
ILLUMINACLIP:/Users/mparida/Software/Trimmomatic-0.32/adapters/:2:40:12 SLIDINGWINDOW:5:20 LEADING:10 TRAILING:12 MINLEN:90

Thanks for your reply. I figured out...
Forum: Bioinformatics 12-28-2013, 07:21 PM
Replies: 9
Views: 8,266
Posted By mparida
Trimmomatic 0.32 error

Hi
I am running Trimmomatic 0.32 and I couldn't figure out why the trim log file shows the following for some reads in the reverse pair file:

phred 33
Illumina sequencing reads
...
Forum: Bioinformatics 09-25-2012, 09:17 AM
Replies: 31
Views: 13,576
Posted By mparida
I tried moving the contaminants file to the dir...

I tried moving the contaminants file to the dir Trimmomatic-0.22/ and it is working. Thanks.
Forum: Bioinformatics 09-25-2012, 09:06 AM
Replies: 31
Views: 13,576
Posted By mparida
I tried using the new trimmomatic and foudnthie...

I tried using the new trimmomatic and foudnthie error
java -classpath trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -phred64 ~/Oiko_otogenetics/index45_TCATTC_L001_R1_001.fastq...
Forum: Bioinformatics 08-22-2012, 03:45 PM
Replies: 2
Views: 2,980
Posted By mparida
Hi I think the kmer contents of my data is...

Hi
I think the kmer contents of my data is pretty darn bad. Is there anyway to filter them or trim them from my data and analyze them separately.
Any useful comment is highly appreciated.
Showing results 1 to 15 of 15

 


All times are GMT -8. The time now is 03:06 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO