User: bassanio

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bassanio20
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Posts by bassanio

<prev • 18 results • page 2 of 2 • next >
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Comment: C: Bowtie2 Alignment summary
... Hi, Thank you.. I didnt noticed that.  What I would like to do is to fetch the unaligned reads. if I use --un-conc I get 413631 reads but its like 87% of total reads by my overall alignment rate is 69.22%. if I use --un I dont get any results. So how to fetch those reads(PE) that are not mapped. ...
written 4.8 years ago by bassanio20
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Bowtie2 Alignment summary
... Given below is a summary of Bowtie2 alignment result of mapping transcriptome data to REF genes. Command used : bowtie2 -q -N 1 -p 8 -x REF/REFgene.fasta -1 DATA1/S1_1.fastq -2 DATA1/S1_2.fastq --al-conc Sample_unmapped.fastq -S REF/Bowtie_Result/REF/S1.sam Alignment summary: 474285 (100.00%) wer ...
reads bowtie2 alignment mapping rna-seq written 4.8 years ago by bassanio20 • updated 4.8 years ago by Devon Ryan95k
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Comment: C: Values used for calculating FPKM Value
... If I use the same transcript data and alligned with another genome(B) where aligned reads is 9M and then if I do a DeSeq between Sample A(8M) mapped reads and Sample B(9M) mapped reads then the data is Skewed more towards Sample A as the normallization  value is not same between SampleA and Sample ...
written 4.8 years ago by bassanio20
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Values used for calculating FPKM Value
... Dear All, I had got a Transcriptome Library with 10M PE reads( R1->10M & R2 ->10M ).  When I mapped the same to the genes from a particular genome using Bowtie2  80% of them mapped (8M). Now I need to calculate the Expression rate for these genes. For calculating the FPKM Value I use the ...
rpkm fpkm bowtie written 4.8 years ago by bassanio20 • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Bowtie2 : aligned result read count not matching with sam Read count
... The input file is a metagenome sequences in fasta format. ...
written 5.1 years ago by bassanio20
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Comment: C: Bowtie2 : aligned result read count not matching with sam Read count
... That is because currently I am looking into a single gene of a whole data set. ...
written 5.1 years ago by bassanio20
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Bowtie2 : aligned result read count not matching with sam Read count
... bowtie2 -f -N 1 -p 8 -x REF.fa -1 sample01_1.fasta -2 sample01_2.fasta -S sample01.sam --al sample01_al.fasta --al-conc sample01_alcon.fasta 9260783 reads; of these:   9260783 (100.00%) were paired; of these:     9260311 (99.99%) aligned concordantly 0 times     472 (0.01%) aligned concordantly ex ...
bowtie2 alignment rpkm sam bioinformatics written 5.1 years ago by bassanio20
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How to run tophat without gff file for bacterial genome
... I would like to find the RNA seq differential expression against bacterial genomes with out gff /gtf files. I used the following commands: tophat -p 8 -i 1 -m 2  --max-insertion-length 0 --max-deletion-length 0 -o STA3_WG  Geneome1_WG.fa  R1.fastq R2.fastq And It throws error: [2014-12-17 14:47:5 ...
tophat gene expresssion rna-seq bacterial written 5.5 years ago by bassanio20 • updated 12 months ago by Biostar ♦♦ 20

Latest awards to bassanio

Scholar 8 months ago, created an answer that has been accepted. For A: DMRcate: How to get Cpgids present in the DMR
Scholar 8 months ago, created an answer that has been accepted. For A: DMRcate: How to get Cpgids present in the DMR
Great Question 2.3 years ago, created a question with more than 5,000 views. For Bowtie2 Alignment summary
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Bowtie2 : aligned result read count not matching with sam Read count
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Bowtie2 Alignment summary
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How to run tophat without gff file for bacterial genome
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Values used for calculating FPKM Value

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