User: st.ph.n

gravatar for st.ph.n
st.ph.n990
Reputation:
990
Status:
Trusted
Location:
Philadelphia, PA
Last seen:
1 day, 12 hours ago
Joined:
3 years, 5 months ago
Email:
t*******@temple.edu

Posts by st.ph.n

<prev • 352 results • page 1 of 36 • next >
0
votes
1
answer
115
views
1
answers
Comment: C: getorf: Remove Overlapping Open Reading Frames
... what do your ids look like in your fasta? If they have similar patterns, such as different isoforms from Trinity for example, where you want to the longest isoform per gene cluster, I have a scrip that may help. ...
written 1 day ago by st.ph.n990
1
vote
2
answers
207
views
2
answers
Comment: C: processing FASTA file
... Why did you tag R? Others have given some viable options, but you didn't post anything that you had tried using R (i.e. code snippet), or that you *need* to use R. This would be easy with Biopython. ...
written 1 day ago by st.ph.n990
0
votes
3
answers
208
views
3
answers
Comment: C: fasta files: keep only lines containing certain characters + the respective sequ
... This would work if the fasta was a single-line fasta and not multi-line like the OP has. ...
written 1 day ago by st.ph.n990
0
votes
2
answers
142
views
2
answers
Comment: C: Extact specific sequence from a fasta file into multiple files using ID and EC f
... Can you post the error message? Make sure `file_1.txt` is tab-delimited, and doesn't have spaces. > When I printed out the "seqs" part, I found out that the sequences > were not complete Did you linearize your fasta? Is this homework? If so, and you were instructed to use Biopython, you ...
written 1 day ago by st.ph.n990
1
vote
3
answers
166
views
3
answers
Comment: C: Extract nucleotides from fasta file by a single position
... Thanks for the tips, Matt. I should learn more about pyfaidx. Having a single-line fasta to work with is just a preference of mine, otherwise I would read the file in with Biopython. I like also to write parts out so the OP can learn something and understand what's going on, and without knowing the ...
written 3 days ago by st.ph.n990
0
votes
3
answers
166
views
3
answers
Answer: A: Extract nucleotides from fasta file by a single position
... A Python solution. [Linearize][1] your fasta file, if it has more than one line per sequence. Save this code as `get_pos.py`. Change the names of `pos.txt` to your tab-delimited file, and `input.fasta` to the name of your fasta file. Run as python `get_pos.py > nucl_at_pos.txt`. `nucl_at_pos.txt` ...
written 3 days ago by st.ph.n990
0
votes
0
answers
98
views
0
answers
Comment: C: Genome guided assembly with Trinity using STAR genome index
... Yes, the sorted bam file. Snippet from the tutorial page, referenced above: > Users must provide read alignments to Trinity as a coordinate-sorted > bam file. Use GSNAP, TopHat, STAR or other favorite RNA-Seq read > alignment tool to generate the bam file, and be sure it's coordinate > ...
written 4 days ago by st.ph.n990
0
votes
0
answers
98
views
0
answers
Comment: C: Genome guided assembly with Trinity using STAR genome index
... You can provide the BAM file. I'm not sure if Trinity will complain if it is in SAM format. See [here][1] for tutorial. Make sure you sort you BAM/SAM file with `samtools sort` Ex. Trinity --genome_guided_bam rnaseq.coordSorted.bam \ --genome_guided_max_intron 10000 \ ...
written 5 days ago by st.ph.n990
1
vote
0
answers
101
views
0
answers
Comment: C: GeneMark-ES exits with "error, file not found: info/training.fna"
... You might want to open a new question, and reference this one. ...
written 5 days ago by st.ph.n990
0
votes
0
answers
111
views
0
answers
Comment: C: Can I get BLAST results from commandline BLAST+ in complete and aligned FASTA fo
... What sequences are you blasting? Sounds more like you want a multi-sequence alignment. ...
written 8 days ago by st.ph.n990

Latest awards to st.ph.n

Guru 3 days ago, received more than 100 upvotes.
Scholar 10 days ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 4 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 11 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Popular Question 9 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 10 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Scholar 11 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Supporter 11 months ago, voted at least 25 times.
Centurion 13 months ago, created 100 posts.
Popular Question 14 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 14 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 16 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 17 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 18 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 21 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 21 months ago, created a question with more than 1,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 23 months ago, created a question with more than 1,000 views. For Printing Out Hash (Dictionary) Using Hash Class Python
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Upper Triangular Matrix From Array --Python
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Finding Min Value In List Of Lists -- Python -- Without Numpy
Scholar 2.9 years ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 477 users visited in the last hour