User: liz.marjory

gravatar for liz.marjory
liz.marjory10
Reputation:
10
Status:
New User
Location:
Spain/Experimental Station of Zaidin
Last seen:
1 week, 6 days ago
Joined:
1 year, 4 months ago
Email:
l**********@gmail.com

phD Fellow

Posts by liz.marjory

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
185
views
1
answers
Comment: C: Bacterial RNAseq - Help for beginner
... I got the GTF file from rast annotation server ##gff-version 3 tig00000001 FIG CDS 190 300 . + 1 ID=fig|83263.11.peg.1;Name=hypothetical protein tig00000001 FIG CDS 892 1479 . + 1 ID=fig|83263.11.peg.2;Name=hypothetical protein tig00000001 FIG CDS 1839 196 ...
written 5 weeks ago by liz.marjory10
0
votes
1
answer
185
views
1
answers
Comment: C: Bacterial RNAseq - Help for beginner
... Thanks, the DESeq2 workflow is very detailed But they start using Salmon. I can't do that because I don't have a previous reference transcriptome. Think that necessarily I have to pass by alignment step and start from my genome fasta file. My problem is about the count step, using HTSeq. I don't kno ...
written 5 weeks ago by liz.marjory10
0
votes
1
answer
185
views
1
answers
Comment: C: Bacterial RNAseq - Help for beginner
... Thanks for the links! I tried to use Galaxy but I couldnt upload the fq files (8 files 500MB each one). They seem to be to much heavy ...
written 5 weeks ago by liz.marjory10
0
votes
1
answer
185
views
1
answers
Comment: C: Bacterial RNAseq - Help for beginner
... I have 2 conditions (2 replicates each one) Control and Stress. I have to found wich genes are expressed differentially for my bacteria ...
written 5 weeks ago by liz.marjory10
0
votes
1
answer
185
views
1
answers
Comment: C: Bacterial RNAseq - Help for beginner
... Hi ATpoint This is the command lines for bowtie and htseq bowtie2 -x /home/liz/RNASEQBA135/genoma/aminobacter_index -1 control_rep1_1_paired.fq.gz -2 control_rep1_2_paired.fq.gz -S control_rep1_paired.sam samtools view -Sb control_rep1_paired.sam > control_rep1_paired.bam samtools sort control_ ...
written 5 weeks ago by liz.marjory10
1
vote
1
answer
185
views
1
answer
Bacterial RNAseq - Help for beginner
... Hi everyone I just begin with the analysis of my RNAseq data. I have my own reference genome and its annotated file. I´ve been reading and I decided to use the following pipeline: FastQC ->Trimmomatic -> Bowtie2 -> HTSEQ But, I´ve had some problems, for example My reads have good qua ...
bacteria bioinformatic next-gen rna-seq written 5 weeks ago by liz.marjory10 • updated 5 weeks ago by ahmad mousavi480
1
vote
1
answer
1.3k
views
1
answers
Comment: C: Help required for Bacterial RNAseq data
... Thanks Atpoint for the advices! Was really useful I´ve been reading and I found the SPARTA pipeline. I will try. ...
written 8 weeks ago by liz.marjory10
0
votes
1
answer
1.3k
views
1
answers
Comment: A: Help required for Bacterial RNAseq data
... Hi, I just begin in the RNA seq analysis field and I am working with bacteria as well. Did you find the right pipeline? I am looking for the better tool for aligment step ...
written 8 weeks ago by liz.marjory10
0
votes
1
answer
342
views
1
answers
Comment: C: find data examples to practice INSeq analysis
... Great!!! Thank you ! ...
written 16 months ago by liz.marjory10
2
votes
1
answer
342
views
1
answer
find data examples to practice INSeq analysis
... Hi everybody!!! I am working for first time with transposon insertions by INSeq analysis. So I want to learn how to process and analyce the data, I have been reading and I could find pipelines and papers really usefull but I would like to practice before to receive my owns reads. I know that is ...
transposoninsertions data ngs linux inseq written 16 months ago by liz.marjory10

Latest awards to liz.marjory

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1807 users visited in the last hour