ERROR :: Oligos file, rmap and baitmap production (DpnII enzyme HICUP)

Assignee - chicagoTeam

Dear all,

a) I start by producing the oligos file :

```

Produce_oligo_file % python design.py Capture -f /User/mm10.fa -g mm10 -b ChICregion.bed -e DpnII --blat

```

b) and then try to make the input files needed :

‌

```

perl create_baitmap_rmap.pl digest_file oligo_seqs.fa

```

‌

I got an error (1) producing the oligo file in a), and a second error (2) while trying to run the .pl point b).

I list them below :

‌

(1) :

```

Produce_oligo_file % python design.py Capture -f /User/mm10.fa -g mm10 -b ChICregion.bed -e DpnII --blat

Loading reference fasta file...

...complete

Generating oligos...

...complete.

Wrote oligos to oligo_seqs.fa

Checking for repeat sequences in oligos, with RepeatMasker...

...complete. Output written to oligo_seqs.fa.out

Aligning oligos to the genome, with BLAT...

...complete. Output written to blat_out.psl

Traceback (most recent call last):

File "design.py", line 549, in <module>

c.extract_repeats().calculate_density().write_oligo_info()

File "/Users/...../tools.py", line 146, in extract_repeats

with open('.'.join((self.fasta, 'out'))) as repeats_file:

FileNotFoundError: [Errno 2] No such file or directory: 'oligo_seqs.fa.out'

```

(2) :

```

perl create_baitmap_rmap.pl digest_file oligo_file

‌

Use of uninitialized value $start in subtraction (-) at create_baitmap_rmap.pl line 130, <OLIGO> line 1.

Use of uninitialized value $end in subtraction (-) at create_baitmap_rmap.pl line 130, <OLIGO> line 1.

Use of uninitialized value $start in addition (+) at create_baitmap_rmap.pl line 130, <OLIGO> line 1.

Could not find '>chr3:65194531-65194601-65194531-65197519-L0' in digest_fragments hash - the digest file and oligo probes file appear to be incompatible.

```

I attached the small files produced/employed.

Here as well some lines of the Hicup digested .txt file (I can’t fully upload because bigger than 100 Mb).

Genome:mm10 Restriction_Enzyme1:DpnII [^GATC] Restriction_Enzyme2:None Hicup Digester version 0.8.3
Chromosome Fragment_Start_Position Fragment_End_Position Fragment_Number RE1_Fragment_Number 5'_Restriction_Site 3'_Restriction_Site
chr1 1 3000190 1 1 None Re1
chr1 3000191 3000812 2 2 Re1 Re1
chr1 3000813 3001047 3 3 Re1 Re1
chr1 3001048 3001118 4 4 Re1 Re1
chr1 3001119 3001794 5 5 Re1 Re1
chr1 3001795 3003208 6 6 Re1 Re1
chr1 3003209 3003262 7 7 Re1 Re1
chr1 3003263 3003349 8 8 Re1 Re1
chr1 3003350 3003412 9 9 Re1 Re1
chr1 3003413 3003575 10 10 Re1 Re1
chr1 3003576 3003600 11 11 Re1 Re1
chr1 3003601 3004012 12 12 Re1 Re1

‌

What am I doing wrong? Many thanks for your help!

MZ

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