User: grant.hovhannisyan

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Posts by grant.hovhannisyan

<prev • 160 results • page 1 of 16 • next >
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Comment: C: Extract gene names from a particular cluster from pheatmap
... Thanks! For some reason only cubeupload works for me. ...
written 6 days ago by grant.hovhannisyan730
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Comment: C: Extract gene names from a particular cluster from pheatmap
... Hi Kevin, Thanks for reply! Yes I have seen that post before, but as far as I understand at some point you should do some manual inspection to see where the `cutree` cuts the tree and whether it corresponds to the cluster I need (and since there are a lot of genes I thought it might be problematic). ...
written 6 days ago by grant.hovhannisyan730
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Comment: C: Extract gene names from a particular cluster from pheatmap
... Ah, thanks @genomax, wan't aware about this functionality. ...
written 7 days ago by grant.hovhannisyan730
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Comment: A: Extract gene names from a particular cluster from pheatmap
... I hope @Kevin_Blighe will hear me :) ...
written 7 days ago by grant.hovhannisyan730
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Comment: C: strange htseq-count result
... To save your time and shorten the pipeline, you can use STAR's `--quantMode` option (have a look in manual). It will generate exactly the same read-counts as htseq-count (note that probably this would not solve the issue you posted here). ...
written 7 days ago by grant.hovhannisyan730
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Comment: C: RNAseq raw data for expression analysis
... The speed of downloading obviously depends on internet connection. But to speed up fetching you can use aspera https://www.ncbi.nlm.nih.gov/books/NBK242625/ ...
written 9 days ago by grant.hovhannisyan730
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Comment: C: RNAseq raw data for expression analysis
... How exactly have you download the data? For me `fastq-dump --split-3 SRR925687` worked perfectly well downloading paired end reads (each file is 8.4 Gb) ...
written 9 days ago by grant.hovhannisyan730
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Comment: C: Library type warning in Salmon
... Sorry, and one more question. I got this warning, `[warning] Only 4289407 fragments were mapped, but the number of burn-in fragments was set to 5000000.` Mapping rate is 64 %. Should I just ignore that warning? ...
written 11 days ago by grant.hovhannisyan730
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Comment: C: Library type warning in Salmon
... Hi Rob, Thanks for swift reply and explanation. The data I am working with is a bit tricky. We used a specific enrichment technology to enrich lncRNAs from human samples, and then basically sequenced only those enriched lncRNAs and got our fastq files. Then I have run Salmon on transcriptome which ...
written 11 days ago by grant.hovhannisyan730
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Library type warning in Salmon
... Hi Biostars, I have run Salmon software for RNAseq data analysis and got the warning message Greater than 5% of the fragments disagreed with the provided library type; check the file: Pool9_21565_GTTTCG_quant/lib_format_counts.json for details `lib_format_counts.json` file looks like "r ...
rnaseq salmon library-type written 11 days ago by grant.hovhannisyan730 • updated 11 days ago by Rob2.3k

Latest awards to grant.hovhannisyan

Scholar 4 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 7 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Scholar 8 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Centurion 8 weeks ago, created 100 posts.
Scholar 9 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 9 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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