User: priya.saxena
priya.saxena • 0
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Posts by priya.saxena
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... Hello Everyone
I am trying to generate transcriptomes using Stringtie and Stringtie-merge tools and getting error like:
Details
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
Tool generated the following standard error:
Error: no valid ID fo ...
written 15 days ago by
priya.saxena • 0
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15 days ago by
lieven.sterck ♦ 9.5k
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... Thank you so much. I am extremely sorry for so much trouble.
I am new to this field and trying to learn. Thank you so much for your guidance I really appreciate . ...
written 18 days ago by
priya.saxena • 0
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... By compare I meant I have 3 samples and one of them is control, I need to compare the differential genes expression in both the samples with respect to my control.
Moreover for each sample I have three replicates which I need to normalize. ...
written 18 days ago by
priya.saxena • 0
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... Thank You so much.
can we compare 3 conditions at a time ?
I am getting option for comparing two condition at a single time. ...
written 20 days ago by
priya.saxena • 0
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... Hello Everyone,
I am trying to analyze rna-seq (paired-end) data generated from illumina, can anyone suggest me which tool for mapping will be best for it, I tried Bowtie-2 but unable to compare the results as I have 3 conditions and three replicates of each sample.
Thank You ...
written 20 days ago by
priya.saxena • 0
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... Thank You so much
I will try this and let you know. ...
written 24 days ago by
priya.saxena • 0
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... Yes, I used the reference genome and then I did the mapping with Bowtie2 to generate a BAM file. This BAM file and the gtf file from NCBI RefSeq was used as input for Featurecounts. The species used is Desulfovibrio alaskensis G20 from NCBI RefSeq. The FTP link is from where I uploaded GTF and genom ...
written 27 days ago by
priya.saxena • 0
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While using Featurecounts tool, I am getting zero counts for RNA seq reads, It can be due to unmatched chromosome identifiers in BAM and GTF file. Can someone please help me out in making the identifiers same for both the file?
https://ibb.co/10rT9tL
https://ibb.co/414jkhG
Thank You
...
written 27 days ago by
priya.saxena • 0
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... Thank you so much
But i am getting this kind of warning in whole file. ...
written 29 days ago by
priya.saxena • 0
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... Hello Everyone
I am trying to map the pair end reads using Bowtie2, I have formatted the custom reference genome using the format given in link: https://galaxyproject.org/learn/custom-genomes/ (used normalized custom reference file).
There is no error while running the Bowtie2 tool but I am getti ...
written 29 days ago by
priya.saxena • 0
• updated
29 days ago by
_r_am ♦ 32k
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