User: drtamermansour

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Posts by drtamermansour

<prev • 13 results • page 1 of 2 • next >
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Cuffcompare: Sensitivity (Sn) higher than 100
... I compare 2 assemblies using Cuffcompare. Unexpectedly I am getting the exon level sensitivity > 100%. I found the same question on their forum with no answer https://groups.google.com/forum/#!searchin/tuxedo-tools-users/cuffcompare$20sensitivity/tuxedo-tools-users/80oj3jH8juI/t9Cu7cAjAlAJ A ...
cuffcompare rna-seq written 3.1 years ago by drtamermansour40
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Identify read group info for multiplexed samples
... I want to identify the @RG info to add them to the BAM files. I am familiar with the situation where I have multiple libraries of the same sample or when we run the same library on multiple lanes. My question is about multiplexing. Let us say I have 2 samples (S1 and S2).  I prepared both samples a ...
readgroup variant caling written 3.4 years ago by drtamermansour40
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Comment: C: Changing @RG header information in *.bam files using picard
... does this hold true with multiplexed samples?  ...
written 3.4 years ago by drtamermansour40
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Extracting transcripts in gtf from reference with incorporation of variants from vcf
... I have my reference in a fasta format. My gene model generated by Cufflinks in a GTF format and genomic variants in VCF format. I want to extract the fasta sequences of  my transcripts from the reference but modified according to the VCF. My thoughts - if I changed the reference to a new consensus ...
vcf rna-seq getfasta written 3.6 years ago by drtamermansour40
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Answer: A: Low final mapping rate by TopHat in spite of high initial Bowtie mapping
... I found that --prefilter-multihits is the reason why this is happening. I think this is a bug in TopHat because the log files show that only few hundred reads are filtered out as multi hits. I tried TopHat2 version 2.1.0 but the problem is still the same.  ...
written 3.7 years ago by drtamermansour40
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Comment: C: Low final mapping rate by TopHat in spite of high initial Bowtie mapping
... I add the singletons to the end of the R1 file according to TopHat manual. ...
written 3.8 years ago by drtamermansour40
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Low final mapping rate by TopHat in spite of high initial Bowtie mapping
... Hi,  I am running TopHat2/2.0.14 using this code: tophat \ --transcriptome-index "${transcriptome_index}" \ --num-threads 4 \ --output-dir "${output_dir}" \ --coverage-search \ --microexon-search \ --prefilter-multihits \ --library-type "${lib_type}" \ "${Bowtie ...
tophat alignment rna-seq written 3.8 years ago by drtamermansour40
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Reconstruction of complete gene cDNA from Trinity output
... I am done with transcriptome assembly for a non-reference plant using Trinity. The final Trinity.fasta file has more than 70,000 contig. These contigs must include different isoforms or ESTs for the same genes. I want to merge those isofoms to generate a more complete gene cDNA. I can see that EGass ...
est assembly egassembler transcriptome written 4.6 years ago by drtamermansour40
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Comment: C: VelvetOptimiser: optimum cov_cutoff, PE insert stats, 2 Insert Size Libraries, N
... Thank you @SES I have some clarifications on my questions: 1) coverage cutoff: The optimizer has already defined the optimum cutoff but the problem is that it used another value for the final run !! 2) Insert size stats: My problem is that the optimizer output has 2 different insert size for each ...
written 4.6 years ago by drtamermansour40
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VelvetOptimiser: optimum cov_cutoff, PE insert stats, 2 Insert Size Libraries, N's without scaffolding, Using 2 Insert Size Libraries
... I am trying to use VelvetOptimiser to do denovo assembly of a plant. I have 2 libraries; 100PE with insert size ~ 400bp and 150PE mate pair library with 12-18k insert size. I have several questions: A) I tried to do initial assembly with only 1 library (the 100PE with insert size 440bp) like this: ...
velvetoptimiser denovo assembly written 4.6 years ago by drtamermansour40

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Identify The Origin Of Tumor By Rnaseq
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