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Istvan Albert
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Bogdan
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rpolicastro
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Recent Replies
Comment: FastQ: quality string length is not equal to sequence length
by
GenoMax
120k
Can you try aligning the data using `minimap2`? This may be a bug in `STARlong`.
Answer: What do Over-represented Sequences mean in FastQC using RNA-Seq?
by
Istvan Albert
94k
See what the mapping says. Align your data to a reference.
To be honest, your data looks a little suspect, you have too many full adapters…
Comment: What do Over-represented Sequences mean in FastQC using RNA-Seq?
by
GenoMax
120k
> A sample wouldnt have two different types of Adapters so this confuses
> me?
One is a primer and other is an adapter. Those are two diff…
Comment: FastQ: quality string length is not equal to sequence length
by
rpolicastro
9.8k
If it can rescue a read it will do so without discarding it, so try realigning now to see if it worked.
Comment: Converting PLINK binary files into python dataframe
by
zorbax
▴
460
use [the `chunksize` option](https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#iterating-through-files-chunk-by-chunk) when y…
Answer: RSeQC confusing output - Half fails to determine, half is reverse strand
by
Xin
•
0
It's 20 months late, but today I encountered the same problem. Now, I know this problem is caused by annotation files. I use the new versio…
Comment: FastQ: quality string length is not equal to sequence length
by
yvonnehhe
•
0
Thanks for the reply, I used seqkit sana but all the lines passed and it discarded 0 lines.
Comment: Understanding bowtie2 for short reference sequences
by
Istvan Albert
94k
no there are pleny of fast optimal aligners (just that none are suited for large sequences)
pairwise2 in BioPython is fast: https://biopyt…
Comment: In-paralog & out-paralog
by
Dave Carlson
▴
1000
The green circled proteins duplicated in the common ancestor of the species in question, so they are out-paralogs. While the blue circled p…
Comment: In-paralog & out-paralog
by
397975944
•
0
![in&out paralogs][1]
This is the schematic diagram of in-paralogs and out-paralogs provided in the lecture. The question only say design …
Comment: FastQ: quality string length is not equal to sequence length
by
swbarnes2
12k
Well, what does that entry look like in the fastq?
Answer: In-paralog & out-paralog
by
Dave Carlson
▴
1000
Blast alone cannot tell you what kind of homology relationship two proteins share. Some researchers use reciprocal best hits as proxy for …
Answer: creating a txt file with absolute path to each directory
by
Pierre Lindenbaum
149k
find /path/to/root -type f -name "*.db" > out.list
Comment: Confused about which database to use - nt or nr?
by
5heikki
10k
If you have transcripts (3 potential reading frames) it's rather wasteful to do blastx with its 6 reading frames. It's far more computation…
Answer: Confused about which database to use - nt or nr?
by
Jeremy Leipzig
21k
"translated DNA:protein (BLASTX) searches are far far more sensitive than DNA:DNA searches" - Bill Pearson
if you're happy with your bla…
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