User: caggtaagtat

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caggtaagtat290
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Posts by caggtaagtat

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What does the transcript support level (TSL) from ensembl mean?
... Hi, during my search for interesting transcripts, I came across the Trancript support levels (TSL) from ensembl. After extensive goolging, I still am not 100% sure, how it is determint. Do you maybe have a paper with an explenation or a definition for me? Kind regards ...
ensembl tsl annotation written 1 day ago by caggtaagtat290
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Answer: A: STAR indexing gets killed on its own at a particular time (while generating suff
... I think STAR uses a lot of RAM (~30GB), so that could be an issue. You can reduce the RAM requirements with the "sparse" mode, this will make it a little slower thou. ...
written 15 days ago by caggtaagtat290
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Comment: C: Counting reads aligned to forward or reverse strand
... Ok, so using the HTseq-count script, I got a much more believable result, with most reads on the heavy strands. ...
written 6 weeks ago by caggtaagtat290
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Comment: C: Counting reads aligned to forward or reverse strand
... Thank you, I will try to use htseq-count and the RSeQC now. I was just wondering, if I can really access the stranded coverage with these Flags in samtools view or if I got something wrong. ...
written 6 weeks ago by caggtaagtat290
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Counting reads aligned to forward or reverse strand
... Hello, I mapped reads (stranded library prep) with STAR to my reference genome and learned, that you can count reads, which aligned to the forward or reverse strand of the reference seuquence, using the FLAG option. Reads mapped to Forward strand samtools view -c -F 20 FILE.bam >> Outp ...
rna-seq written 6 weeks ago by caggtaagtat290 • updated 6 weeks ago by michael.ante2.6k
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Comment: C: What server do you use?
... Yeah, maybe this is connected to the throtteling of acess from medical facilities ...
written 8 weeks ago by caggtaagtat290
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Answer: A: sortMeRNA before or after adapters trimming ?
... If you are using it for rRNA removal, I would use it after trimming, since I basically maps the reads to the rRNA database and with trimming beforehand, the process should be improved. However be aware, that sometimes it can happen, that a random blank line gets integraded into your data ...
written 8 weeks ago by caggtaagtat290
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Comment: C: How to repair corrupted fastq files after sortmeRNA
... Oh ok. I wasn't aware of that! Luckily it doesn't matter for me, since I trim the reads beforehand and mapping doesn't consider base calling quality. But nevertheless I will have to check all my data, to be sure ...
written 8 weeks ago by caggtaagtat290
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Comment: C: What server do you use?
... Yes I sometimes work in interactive mode, but it usaully takes some time to be able to log in and I therefore just submit jobs ...
written 8 weeks ago by caggtaagtat290
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Comment: C: What server do you use?
... Yes they are great and helped me a lot! They also arranged the collective complaint, to change restictions for medical institutions to the HPC. ...
written 8 weeks ago by caggtaagtat290

Latest awards to caggtaagtat

Centurion 9 weeks ago, created 100 posts.
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Scholar 4 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Supporter 6 months ago, voted at least 25 times.
Appreciated 6 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Appreciated 7 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?

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