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Rahul Nayak answered the question What are the best way to merge paired end reads ?- sahabuddin commented on the blog Important Journals, Blogs and Forums for Bioinformaticians
- sahabuddin posted a new ad in the Opportunity Postdoctoral scholarship in Bioinformatics at KTH
- sahabuddin is now a friend with Radha Agarkar
- Radha Agarkar is now a friend with sahabuddin
- Neel published a blog post Letter of motivation for bioinformatics applicants !Comments
- Shruti Paniwala 1471 days ago
Any Motivation Letter should consist of a short intro defining the program you would like to get.
First, state a clear objective of your future task and the reasons for picking this individual Ph.D. program.
Provide the info regarding your previous scholastic and professional experience. You can also include teaching and research experience, work outside an academic field, and even volunteering, given that all matter, in terms of the abilities and expertise you gained. All your experiences must, in some way, attach to your picked Ph.D. program, as you would need to define just how your scholastic, as well as professional achievements, make you a beneficial candidate for the Ph.D. degree/Research position you are related to.
Your applications are not just sorted out in the same way as any other random application. There are processes involved without which your chances of getting in may be reduced.
There is a demand to recognize if you’re qualified to do a research/degree position while writing an application. Hence, the motivation letter is the perfect insight into what you genuinely are and anticipate doing it justice.
- Rahul Agarwal posted to the wire
- Rahul Agarwal posted to the wire
- Jit published a news post 1mb long DNA with Nanopore technology
- Rahul Nayak published a blog post String graph based genome assembly software and tools !
- Jit created a page Run miniasm assembler on nanopore reads !Comments
- Rahul Nayak 2419 days ago
Here’s the quick and dirty of what was done:
1 Run minimap:
This uses a pre-built set of defaults (the
ava-pbin the code below) for analyzing PacBio data. Minimap only accepts two FASTQ files and you need to map your FASTQ file against itself. So, if you have multiple FASTQ sequencing files, you have to concatenate them into a single file prior to running minimap.minimap2 -x ava-pb -t 23 \ 20170911_oly_pacbio_cat.fastq \ 20170911_oly_pacbio_cat.fastq \ > 20170911_minimap2_pacbio_oly.paf2 Run miniasm:
This uses your concatenated FASTQ file and the PAF file output from the miniasm step. The code below is taken from the example provided in the miniasm documentation; there are other options available.
miniasm \ -f \ /home/data/20170911_oly_pacbio_cat.fastq /home/data/20170911_minimap2_pacbio_oly.paf > /home/data/20170918_oly_pacbio_miniasm_reads.gfa3 Convert miniasm output GFA to FASTA
The FASTA file is needed to re-run minimap in Step 4 below.
awk '$1 ~/S/ {print ">"$2"\n"$3}' 20170918_oly_pacbio_miniasm_reads.gfa > 20170918_oly_pacbio_miniasm_reads.fasta4 Run minimap with default settings
Using the default settings maps the FASTQ reads back to the contigs (the PAF file) created in the fist step. These mappings are required for Racon assembly (Step 5).
minimap2 \ -t 23 \ 20170918_oly_pacbio_miniasm_reads.fasta 20170905_minimap2_pacibio_oly.paf > 20170918_minimap2_mapping_fasta_oly_pacbio.paf5 Run racon
The output file is the FASTA file listed below.
racon -t 24 \ 20170911_oly_pacbio_cat.fastq \ 20170918_oly_pacbio_minimap_mappings.paf \ 20170918_oly_pacbio_miniasm_assembly.gfa \ 20170918_oly_pacbio_racon1_consensus.fastafrom Sam’s Notebook http://ift.tt/2fKBPUN
- Rahul Nayak 1048 days ago
minimap2 –x ava-ont \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ | gzip -1 > ./minimap.paf.gzminiasm -f \ ../../trimming_practical/nanofilt/nanofilt_trimmed.fastq \ ./minimap.paf.gz > miniasm.gfaawk ’/^S/{print “>”$2”\n”$3}’ miniasm.gfa > miniasm.fastaassembly-stats ./miniasm.fastadnadiff -p dnadiff ~/course_data/precompiled/chr17.fasta miniasm.fasta
- Jit bookmarked Biological file format tutorial
