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1d
comment Programs/software to graph biological data
Unless the kind of analysis you do is really "standard" and readily available as a program, a bit of programming may become necessary. Some years ago, I found it practical to use python to perform analyses and generate custom graphical representation via the TikZ package of LaTeX. Now I most often use matplotlib, but this is still python programming. Inkscape is useful to adjust your final figures, but programmatically generating graphical representations allows rapid updates when data or parameters change.
Apr
17
comment Significance of upper-case, lower-case and Ns in UCSC DNA files
How is the number of N's determined ?
Mar
9
comment Why do fetuses have membranes between fingers and toes?
It seems difficult for me to define "easily" in the context of organ development. In any case, the way organs develop is mostly inherited from our ancestors, so "it's easy to do so" and "it's inherited" are not necessarily contradictory statements.
Mar
9
comment What is this creature?
It looks very similar to the grey shrimps that can be catched on sandy beaches of Normandy (on the English Channel).
Mar
4
comment What tool to use to map reads (samtools, sequencher,…)?
If you don't see the reads at large scale, then I'm afraid you cannot know, just using IGV, where to zoom to see them. You need to identify regions of interest with other means. For instance, samtols view -c aln.bam chr1 should give you the number of alignments in chromosome 1 (provided it is named chr1). samtools view -H aln.bam should give you, among other information, the list of chromosomes that you can query (preceded with "SN:").
Feb
14
comment Am I a lobe-finned fish?
I would add "ecological sense" to "common sense". Ecologically, humans are not lobe-finned fish: they do not live in water, and don't use fins for swimming. But their body structures are inherited from animals that did so.
Jan
29
comment Question about SAM CIGAR string
Don't know how to quote properly in a comment. I quoted footnote 10 of the current sam format specification (page 7).
Jan
29
comment Question about SAM CIGAR string
The MD optional flag gives more details regarding the alignment: > The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.
Nov
18
comment What is this dried animal for sale?
I'd guess it's a primate, or a big rodent.
Nov
17
comment Does a DNA sequence has its own derivation tree or pattern?
There are regulatory motif databases, and prediction algorithms for functions in a sequence, but all this is not fully known. Indeed, things are rarely fully regular in biology, so every bioinformatics predictions ideally should be completed with experimental confirmation. Also, the same sequence can sometimes be parsed in various way: a single DNA sequence may encode several proteins, depending on which portions are actually translated into amino-acids. Some keywords you may be interested in: start codon, stop codon, open reading frame, 3'UTR, 5'UTR, binding box.
Nov
4
comment What plant is this?
True, it could also be an Asteraceae, but the texture of the yellow part, the low number and the almost-round shape of the white petal-like parts somehow make me prefer the other hypotheses.
Oct
13
comment What sort of seed pod is this?
Are there any trace of a hole through which a bug could have entered? The content looks messy. Can you isolate seed ?
Oct
12
comment What happened to this seashell?
I'd say that the holes were made by animals. I know some mollusks can make holes on rocks, for instance en.wikipedia.org/wiki/Pholadidae But in the case of this shell, the animals must be much smaller.
Sep
9
comment What is the name of the plant with the down-falling light purple leaves?
The common name in English is "foxglove". Note that they are poisonous.
Jul
15
comment Can someone identify this stinging plant?
It would help if you could add in what country you mother was stung by this plant.
Jul
6
comment Help identify this worm-like thing
Are leeches supposed to like bacon ? I thought they needed fresh blood.
Jul
2
comment What is the name of this bird?
Couldn't it be a juvenile of some well known species ?
Apr
24
comment I have a black tiny bug crawling all over the house
It seems from some of the photos that the "stage 2" have quite thin and long antennae, unlike what I've seen in termite images. Besides, the size is very small, so I wouldn't bet they are termites.
Apr
24
comment I have a black tiny bug crawling all over the house
Can you keep some "stage 1" isolated in a jar with some dust and a tiny drop of water (just guessing what they might feed on) and see if they actually turn into "stage 2" ?
Apr
24
comment I have a black tiny bug crawling all over the house
You write: "once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles". Could it be that they are simply less visible when in the carpet as when on the tiles ?