User: fadhil.abubaker

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Posts by fadhil.abubaker

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Comment: C: Migrating pipeline from TopHat to STAR
... Is it safe to say that TopHat2's results above are wrong and should not be used for any downstream analysis? Does anyone know of a different program that I can use to extract splice junction information? This way I have a third dataset for compare. ...
written 10 days ago by fadhil.abubaker10
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Comment: C: Migrating pipeline from TopHat to STAR
... I did try two-pass mode with STAR but it barely made any difference. It's just that the discrepancy between the two is so large I'm not actually sure which to trust. ...
written 10 days ago by fadhil.abubaker10
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Migrating pipeline from TopHat to STAR
... Hey all, Our current pipeline for alignment and analysis uses TopHat + Cufflinks and we wish to replace TopHat with STAR. We are in particular interested in splice junctions so we ran STAR against a sample and compared both the junctions file from TopHat and STAR. For some reason, TopHat seems to ...
alignment rna-seq written 10 days ago by fadhil.abubaker10 • updated 10 days ago by Ram15k
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Comment: C: Low mapping rate for Tophat2
... In the end rebuilding indices helped a bit but I was still getting low mapping rate. Turns out the fastq files were corrupted and re-downloading them helped. Thanks for everyone's help! ...
written 6 months ago by fadhil.abubaker10
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Comment: C: Low mapping rate for Tophat2
... The files in `/home/fadhil/Bowtie2Index/genome` are all .bt2 files and not fasta. I'm not too sure if this makes any difference. ...
written 6 months ago by fadhil.abubaker10
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Low mapping rate for Tophat2
... Hi, I'm somewhat new to bioinformatics, so please bear with me. I'm running tophat2 on some fastq files using the HG38 as reference. This is the command that I ran: ```tophat2 --b2-sensitive -G /home/fadhil/hg38_ref/lib/hg38.refGene.gtf -p 16 -o /home/data/mcf10_tophat_output /home/fadhil/Bowtie2In ...
software error genome rna-seq written 6 months ago by fadhil.abubaker10 • updated 6 months ago by Carlo Yague3.9k

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