User: Biocode_user

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Biocode_user10
Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
1 year, 4 months ago
Joined:
4 years, 11 months ago
Email:
l************@gmail.com

Posts by Biocode_user

<prev • 17 results • page 1 of 2 • next >
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Comment: C: RNA seq- without a control
... thank you. i will try it ...
written 23 months ago by Biocode_user10
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Comment: C: RNA seq- without a control
... The host genes are already analyzed and already looked into the story of defense genes in the host. Since we have no idea about the parasite, i have started to dig in the parasite side of the story to look for genes that are highly expressed and regulated. This one I don't take into account the var ...
written 23 months ago by Biocode_user10
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Comment: C: RNA seq- without a control
... i am not sure if i explained it clearly. An obligate parasite or holoparasite is a parasitic organism that can not complete its life-cycle without exploiting a suitable host. If an obligate parasite can not obtain a host it will fail to reproduce. (From wiki.) In our case we have the parasite an ...
written 23 months ago by Biocode_user10
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Comment: C: RNA seq- without a control
... I have generated the transcriptome of the pathogen1 and 2 by filtering out the host reads. However inorder to do differential expression and to look for the genes that are activated/repressed during the infection, i suppose the usual way is to have the control reads . The reads that you filter out f ...
written 23 months ago by Biocode_user10
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Comment: C: RNA seq- without a control
... we cannot make a control of the pathogen and sequence them as it always comes only with the host Hence we dont have RNA seq data for the pathogen alone ...
written 23 months ago by Biocode_user10
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RNA seq- without a control
... Hello, I have a pathosystem of host and obligate pathogen. There are three strains of host which is treated with two different strains of pathogens. I have RNA seq reads for these treatments described below and have 3 replicates for each treatment a. Host 1 is treated with Pathogen 1 and Host 2 ...
next-gen deseq2 rna-seq written 23 months ago by Biocode_user10 • updated 23 months ago by Devon Ryan93k
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Bowtie mapping to genome
... Hi, I created a reference of a genome using bowtie-build and i want to map the reads to the genome for which i used bowtie command bowtie2 -x reference -1 left.fq -2 right.fq -S out.sam i am interested in the unmapped reads from it.I am looking for a very strict parameter like having 100 ...
genome mapping bowtie written 2.0 years ago by Biocode_user10 • updated 4 days ago by ATpoint26k
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Comment: C: Picardtools Output of CollectRNAMetrices
... Hello Dan, I just formatted the reflat file and the third column matches exactly as the contig name in bam file. But stil I get the same results. How will the length of the contigs screwing up the calculation? I did not understand your comment on that? ...
written 3.8 years ago by Biocode_user10
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Comment: A: Picardtools Output of CollectRNAMetrices
... for that the output looks like @HD VN:1.0 SO:coordinate @SQ SN:Ec-00_000010 LN:1971 @SQ SN:Ec-00_000020 LN:195 @SQ SN:Ec-00_000030 LN:2802 @SQ SN:Ec-00_000050 LN:871 @SQ SN:Ec-00_000060 LN:360 @SQ SN:Ec-00_000070 LN:964 @SQ SN:Ec-00_000080 LN:1908 @SQ SN:Ec-00_000090 LN:1366 @SQ SN:Ec ...
written 3.8 years ago by Biocode_user10 • updated 3.8 years ago by Dan D7.0k
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Picardtools Output of CollectRNAMetrices
... Hello, I am using picard-tools CollectRNAMetrices to get the read statistics of mapping to exons, and UTRs etc. I am using java -jar /software/shared/apps/x86_64/picard-tools/1.129/picard.jar CollectRnaSeqMetrics REF_FLAT=formatted_chrALL.refflat2 STRAND_SPECIFICITY=NONE INPUT=out.prefix.bam OUT ...
rna-seq written 3.8 years ago by Biocode_user10 • updated 3.8 years ago by Dan D7.0k

Latest awards to Biocode_user

Popular Question 22 months ago, created a question with more than 1,000 views. For Trouble in running Baseml
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bash script to run clustalw and fetching sequences
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Error while mapping reads to assembly using bowtie

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