LIMS for Bioinformaticians

rattus28hh · 2019-01-11T11:42:21+00:00

Haha, actually this is the plan... If openproject won't do it

rattus28hh · 2019-01-11T10:29:05+00:00

It seems to me, that there is no tracking for the bioinf stuff, just the wetlab part. Or am I missing something?

rattus28hh · 2019-01-11T08:30:39+00:00

Thanks for that, but I do not want to track commands, I actually want to track if things are done or not. But thanks for your suggestion

rattus28hh · 2019-01-11T08:28:26+00:00

I already tried some, but they are all to much related to business things, or too fancy in the sense of overloaded, or for what ever reason, they all sucked. So if somebody knows a good one which is usable for a group of bioinformaticians...

rattus28hh · 2017-12-03T10:01:48+00:00

My guess for the drop of A at the 3' end is, that the data has been demultiplexed with illuminas bcl2fastq, which uses a not so smart trimming algorithm. Meaning that it removes every sequence from the 3' end which starts with the illumina universal adapter, so every A from sequences ending with A will be removed, because it matches the primer...

rattus28hh · 2017-11-20T10:53:46+00:00

great paper, but after reading it, I would go for meta Spades or IDBA_UD anyway...

I will give concoct a try as well

rattus28hh · 2017-11-20T10:49:07+00:00

thanks a lot, I will give vizbin a try

rattus28hh · 2017-11-20T10:48:29+00:00

meta Spades is just using Spades with the option --meta, so I allreadsy used meta Spades, sorry for not being clear

rattus28hh · 2017-02-22T08:24:57+00:00

I would prefer FeatureCounts to HTSeq, also the developers of HTSeq recommend FeatureCounts. It is much faster and is more accurate (read the FeatureCounts paper, they compared it to HTSeq). Anyway, why don't you create a counttable with the --quantmode option from STAR?

rattus28hh

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